ibi

[chemistry]

Hello all!!!

I'm just started to use votca and at the moment I'm going threw the
tutorial. But I've got some problem with IBI procedure. In general I
understood what mean every parameter in the "setting.xml" file but I
have a problem when I'm trying to submit the calculation: nothing
happened. Can anyone tell me what exactly I may have missed in the
standart "setting.xml" file for propane. I'll appreciate any advise,
thanks a lot in advance!

Sergio

[Christoph Junghans]

Hi Sergio,

can you be a bit more explicit, what (not) happens?
I quickly tested the propane tutorial:
$ pwd
$HOME/votca/src/tutorials/propane/ibi
$ csg_inverse --options settings.xml #for version 1.1 remove --options
For a more verbose log see: inverse.log
We are doing Method: ibi
Prepare (dir step_000)
Using initial guess from dist A-A.dist.tgt for A-A
...

It seems to work for me.
Which version are you using? (see csg_stat --help)
Which command did you execute to start ibi?

Cheers,

Christoph

2011/6/6 chemistry <donet...@gmail.com>:

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>
>

--
Dr. Christoph Junghans
Votca Core Developer

Web: http://www.votca.org

[chemistry]

Hello, Christoph!!!

Thanks for the quick reply.

Under "nothing happens" I meant that after execution the command

$ csg_inverse settings.xml (I'm using version 1.1.1)

I have message: "end". And I do not have any created dir (step_000) or
files (like inverse.log...).
But when I'm using

$ csg_stat --top topol.tpr --trj traj.xtc --options settings.xml --cg
propane.xml

for computing RDF's for propane it works with the same "settings.xml"
file and I have created A-A.dist.new for A-A...
Is it possible that I have some problem with a link to the gromacs and
VOTCA cannot start iterative procedure?

Thanks a lot in advance.
Sergio

On Jun 6, 10:56 am, Christoph Junghans <jungh...@votca.org> wrote:
> Hi Sergio,
>
> can you be a bit more explicit, what (not) happens?
> I quickly tested the propane tutorial:
> $ pwd
> $HOME/votca/src/tutorials/propane/ibi
> $ csg_inverse --options settings.xml #for version 1.1 remove --options
> For a more verbose log see: inverse.log
> We are doing Method: ibi
> Prepare (dir step_000)
> Using initial guess from dist A-A.dist.tgt for A-A
> ...
>
> It seems to work for me.
> Which version are you using? (see csg_stat --help)
> Which command did you execute to start ibi?
>
> Cheers,
>
> Christoph
>

> 2011/6/6 chemistry <donets1...@gmail.com>:

>
>
>
> > Hello all!!!
>
> > I'm just started to use votca and at the moment I'm going threw the
> > tutorial. But I've got some problem with IBI procedure. In general I
> > understood what mean every parameter in the "setting.xml" file but I
> > have a problem when I'm trying to submit the calculation: nothing
> > happened. Can anyone tell me what exactly I may have missed in the
> > standart "setting.xml" file for propane. I'll appreciate any advise,
> > thanks a lot in advance!
>
> > Sergio
>
> > --
> > You received this message because you are subscribed to the Google Groups "votca" group.
> > To post to this group, send email to vo...@googlegroups.com.
> > To unsubscribe from this group, send email to votca+un...@googlegroups.com.

> > For more options, visit this group athttp://groups.google.com/group/votca?hl=en.

[Christoph Junghans]

2011/6/7 chemistry <donet...@gmail.com>:

> Under "nothing happens" I meant that after execution the command
> $ csg_inverse settings.xml (I'm using version 1.1.1)
> I have message: "end". And I do not have any created dir (step_000) or
> files (like inverse.log...).

Very strange! Please run
$ bash -x `which csg_inverse` settings.xml
and post the output.

Cheers,

Christoph

> For more options, visit this group at http://groups.google.com/group/votca?hl=en.

[chemistry]

After run

$ bash -x `which csg_inverse` settings.xml

I've got this message:

"bash: csg_inverse:: No such file or directory"

I tried to set the path to the "csg_inverse" and gromacs directly in
the "settings.xml" but it does not help.

On Jun 7, 1:22 pm, Christoph Junghans <jungh...@votca.org> wrote:
> 2011/6/7 chemistry <donets1...@gmail.com>:> Under "nothing happens" I meant that after execution the command

[chemistry]

On Jun 8, 11:59 am, chemistry <donets1...@gmail.com> wrote:
> After run
>
> $ bash -x `which csg_inverse` settings.xml
>
> I've got this message:
>
> "bash:  csg_inverse::  No such file or directory"
>

> I tried to set the path for the "csg_inverse" and "gromacs" directly in

[Christoph Junghans]

2011/6/8 chemistry <donet...@gmail.com>:

> After run
> $ bash -x `which csg_inverse` settings.xml
> I've got this message:
> "bash:  csg_inverse::  No such file or directory"

It seems like your installation is broken. How did you install your
VOTCA version?
Is there a csg_inverse installed?

Cheers,

Christoph

> For more options, visit this group at http://groups.google.com/group/votca?hl=en.

[chemistry]

Seems that yes. In the folder "/votca-tools-1.1.1/bin/" I have
installed "csg_inverse" and all another tools.
For installation of VOTCA I used "./build.sh". I installed
additionally GROMACS with shared lib (*.so), because at the beginning
it was a problem.



On Jun 8, 1:38 pm, Christoph Junghans <jungh...@votca.org> wrote:
> 2011/6/8 chemistry <donets1...@gmail.com>:> After run

[Victor Ruehle]

Hey,

did you source your VOTCA installation?

source /votca-tools-1.1.1/bin/VOTCARC.bash

And if you manually installed gromacs that as well? If you still don"t
get it running

bash -x /votca-tools-1.1.1/bin/csg_inverse settings.xml

and send the output.

Cheers,
Victor

2011/6/9 chemistry <donet...@gmail.com>:

[chemistry]

Thanks a lot for advice. Now ibi procedure works.

On Jun 9, 8:31 pm, Victor Ruehle <rue...@votca.org> wrote:
> Hey,
>
>  did you source your VOTCA  installation?
>
> source /votca-tools-1.1.1/bin/VOTCARC.bash
>
> And if you manually installed gromacs that as well? If you still don"t
> get it running
>
> bash -x  /votca-tools-1.1.1/bin/csg_inverse settings.xml
>
> and send the output.
>
> Cheers,
> Victor
>

> 2011/6/9 chemistry <donets1...@gmail.com>:

[chemistry]

I have one addition question about the ibi procedure. I have a polymer
chain and I'm doing ibi for non-bonded interactions. How can I exclude
the bond part from the RDF? Because in my case I have all the same
beads in the backbone chain of my polymer and when I'm calculating the
RDF it does not correspond to the purely non-bond interactions. This
RDF except the non-bonded part includes the bonded part.

Thanks a lot in advance.
Sergio

[Victor Rühle]

Hey,

Can you please describe you problem in more details, what exactly did
you try? Are you referring to calculating the target rdf, or the rdf in
the iterations?

We introduced proper exclusion handling in version 1.1, so it should
work. You can check whether exclusions are read correctly by:

csg_dump --top topol.tpr --excl

or if you use csg_stat to calculate target rdf:

csg_dump --top topol.tpr --cg mappin.xml --excl

If you use g_rdf, you have to specify the topology -s topol.tpr in
addition to an index file.

A brief side-note:
Be aware, that for the reference rdf and that during the iterations, the
exact identical normalization should be used (there is room for some
discrepancy, however as far as i could see it's more problematic for IMC
than for IBI). Therefore better use the same program for both (csg_stat
to calculate reference). In version 1.2, which was released yesterday,
we have adjusted the normalization to be identical to g_rdf in gromacs 4.5.

Victor

[chemistry]

I'm trying to calculate the target rdf for polymer system with the
"csg_stat" and also I'm interested to calculate the rdf in the
iterations:

csg_stat --top topol.tpr --trj traj.xtc --options settings.xml --cg

mapping.xml

I have P3HT system. Every monomer divided on the three beads.
Thiophene ring represented the first bead and hexyl chain divided on
the two beads - each bead include three carbon atoms.

in the settings.xml file I specified the types of the beads which are
the same like in the mapping.xml:

.............
<non-bonded>
<!-- name of the interaction -->
<name>P1-P1</name>
<!-- types involved in this interaction -->
<type1>A</type1>
<type2>A</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>1.36</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>P1-P1.dist.tgt</target>
<!-- update cycles -->
<do_potential>1 0 0</do_potential>
<!-- additional post processing of dU before added to potential
-->
<post_update></post_update>
<!-- additional post processing of U after dU added to potential
-->
<post_add></post_add>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_P1_P1.xvg</table>
</gromacs>
</inverse>
</non-bonded>
...............


---mapping.xml---:

<cg_molecule>
<name>P3HT</name>
<ident>Protein_X</ident>
<topology>
<cg_beads>
<cg_bead>
<name>S1</name>
<type>A</type>
<symmetry>1</symmetry>
<mapping>A</mapping>
<beads> 1:BBB:S01 1:BBB:C01 1:BBB:C02 1:BBB:H01 1:BBB:C03
1:BBB:C04 1:BBB:H02 </beads>
</cg_bead>
................

Also I specified all <bonds> and <angles> and <weights>. It works
well, but the second nearest neighbor does not excluded from the rdf.
Seems that the exclusion works just for the first nearest neighbor. Is
it possible to exclude this interaction from the rdf?

[Victor Ruehle]

Hmm, are you sure that all the beads which should be excluded are
part of an angle definition? If yes, Votca should exclude them
automatically..

I'm doing a very similar thing and it worked for me. Will check
tomorrow whether there might be a new bug.However, third or fourth
nearest neighbors should still be visible, there is no option so far
to exclude all beads in the molecule. I could add that if necessary.

Please verify if the peaks you observe really correspond to second
nearest neighbors, and if yes whether you have this particular angle
defined in the mapping. Also check csg_dump --excl

2011/6/21 chemistry <donet...@gmail.com>:

[chemistry]

Hey, Victor!

Thanks a lot for advice, I checked all again and I found the mistake
in my mappin.xml file. I fixed it and now it works well.
Is it something important in the calculation of the rdf in the
iterations for such a systems?

Thanks a lot in advance.
Sergio

On Jun 21, 6:02 pm, Victor Ruehle <rue...@votca.org> wrote:
> Hmm, are you sure that  all the beads which should be excluded are
> part of an angle definition?  If yes, Votca  should exclude them
> automatically..
>
> I'm doing a very similar thing and it worked for me. Will check
> tomorrow whether there might be a new bug.However, third or fourth
> nearest neighbors should still be visible, there is no option so far
> to exclude all beads in the molecule. I could add that if necessary.
>
> Please verify if the peaks you observe really correspond to second
> nearest neighbors, and if  yes whether you have this particular angle
> defined in the mapping.  Also check csg_dump --excl
>

> 2011/6/21 chemistry <donets1...@gmail.com>:

> ...
>
> read more »

[Christoph Junghans]

Hi Sergio,

2011/6/22 chemistry <donet...@gmail.com>:

> Thanks a lot for advice, I checked all again and I found the mistake
> in my mappin.xml file. I fixed it and now it works well.
> Is it something important in the calculation of the rdf in the
> iterations for such a systems?

Usually one don't want to consider pairs of beads, which interact via
a bonded potential, for the rdf.
The reason is that the rdf is used to calculate the non-bonded
interaction and so only the pairs which interact non-bonded should go
in the rdf.

However in some cases it is useful to calculate the rdf with different
exclusions than the simulation was performed. (the
cg.inverse.gromacs.rdf.topol option in the xml setting file, see the
manual)

Cheers,

Christoph

> For more options, visit this group at http://groups.google.com/group/votca?hl=en.

[chemistry]

Thanks a lot for the previous advices!

I have one more question about table_*.xvg. Can you explain please how
exactly did you create all tables for the propane which you used for
the ibi-procedure (table.xvg, table_a1.xvg, table_b1.xvg). I did the
post-processing of the potentials (bond and angle) and I've got the
same shape for the potentials but much more higher value for the y-
axis. The distribution functions and potentials for bond and angle are
the same like in your presentation. Did I do something wrong or is it
something else what I should know? And which role plays table.xvg in
this case?

Thanks a lot in advance,
Sergio.

On Jun 23, 11:34 am, Christoph Junghans <jungh...@votca.org> wrote:
> Hi Sergio,
>

> 2011/6/22 chemistry <donets1...@gmail.com>:> Thanks a lot for advice, I checked all again and I found the mistake

> ...
>
> read more »

[Christoph Junghans]

Hi Sergio,

the potentials have to look similar around the minimum. The region
left and right are usually extrapolated and the exact form of the
extrapolation does not matter much as the appearance of these values
is exponentially suppressed (exp -E/k_bT).
Make sure that the area {U_min..U_min+k_b T} is correct.

Technically what I do to obtain table_b1.xvg is:
-calculate the distribution with csg_stat / csg_boltzmann
-calculate the potential using awk
$ awk -v kbt=NUMBER '{print $1,($1>0)?-kbt*log($2/$1/$1):"nan"}'
bond.dist.new > bond.pot.new
-take a look at the potential and cut it down to the well-sampled region
-convert it to gromacs format (this was reworked in VOTCA 1.2, before
the extrapolation had to be done by hand)
$ csg_call --options bond.xml --ia-type bonded convert_potential
gromacs bond.pot.new2 table_b1.xvg
where bond.xml looks like this:
<cg>
<inverse>
<program>gromacs</program>
<gromacs>
<pot_max>1e8</pot_max>
<table_end>3</table_end>
<table_bins>0.002</table_bins>
</gromacs>
</inverse>
</cg>

table.xvg is used to calculate the interactions for all pairs, which
do not appear in energygrp_table (in the mdp file).
If all pairs are covered by energygrp_table combinations you can use
any table, but I would use a table filled with zeros.
table.xvg can be useful in cases when you want to mix IBI tables with
a standard force field, then table.xvg should be the default 6-12 LJ
table ($GMXDATA/gromacs/top/table6-12.xvg)

Cheers,

Christoph

2011/6/26 chemistry <donet...@gmail.com>:

[chemistry]

I calculated the potential with awk and with csg_boltzmann. It gives
the same shape of the curves but in the case when I used awk the
minimum of the potential has negative value. Should I shift the
minimum of the potential to zero? Does csg_boltzmann do it
automatically?

Thanks a lot in advance,
Sergio

> 2011/6/26 chemistry <donets1...@gmail.com>:

> ...
>
> read more »

[Christoph Junghans]

You can shift the minimum to zero, it will not change the simulation
result (except for a energy offset).
In VOTCA 1.2 the shifting is done automatically if you are using
'csg_call convert_potential gromacs'

Notice that for angles csg_boltzmann calculates everything in rad,
while gromacs (xvg files) wants degrees, so double check the scale of
the x values again.

Cheers,

Christoph

2011/6/27 chemistry <donet...@gmail.com>:

[chemistry]

In this case I have to multiply x value (rad) on (180/3.14) and
afterwords I can use this distribution function for getting the
potential and if it's not zero just simply shift it to zero?

On Jun 27, 3:20 pm, Christoph Junghans <jungh...@votca.org> wrote:
> You can shift the minimum to zero, it will not change the simulation
> result (except for a energy offset).
> In VOTCA 1.2 the shifting is done automatically if you are using
> 'csg_call convert_potential gromacs'
>
> Notice that for angles csg_boltzmann calculates everything in rad,
> while gromacs (xvg files) wants degrees, so double check the scale of
> the x values again.
>
> Cheers,
>
> Christoph
>

> 2011/6/27 chemistry <donets1...@gmail.com>:

> ...
>
> read more »

[Christoph Junghans]

Actually I would scale the potential, because for angles
U=-kbt*log(dist/sin(angle)) and this normalization is done by csg_boltzmann.

For the normalizations, see eq. 5 of the VOTCA paper
(<http://dx.doi.org/10.1021/ct900369w>)

Cheers,

Christoph

2011/6/27 chemistry <donet...@gmail.com>:

[Victor Ruehle]

Hey,

i also use csg_boltzmann, the tab command (dont forget tab set scale
bond / tab set scale angle for bond/angles). some of my examples (the
.pot files are the output of csg_boltzmann):
bonds:
cp ../../pot/AB_bond.pot .
sed -e '1,5d' -e 's/$/ i/' AB_bond.pot | tac | sed -e '1,4d' | tac >
AB.cut ; cut bad sampled regions at the boundaries
csg_call table smooth AB.cut AB.smooth
csg_resample --in AB.smooth --out AB.refined --grid 0::0.001:0.5
csg_call table extrapolate --function quadratic AB.refined AB.pot.cur
csg_call --ia-type bonded --ia-name AB --options ../convert.xml
convert_potential gromacs

angles:
cp ../../pot/ABC_angle.pot .
#sed -e '1,3d' -e 's/$/ i/' ABC_angle.pot | tac | sed -e '1,3d' | tac > ABC.cut
sed -e 's/$/ i/' ABC_angle.pot | tac | sed -e '1,2d' | tac > ABC.cut
csg_call table smooth ABC.cut ABC.smooth
csg_resample --in ABC.smooth --out ABC.refined --grid 0::0.001:3.141592654
csg_call table extrapolate --function quadratic --region left
ABC.refined ABC.refined
csg_call table extrapolate --function linear --region right
ABC.refined ABC.refined
awk '{print $1/3.141592654*180.0,$2}' ABC.refined > ABC.pot.cur
csg_call --ia-type angle --ia-name ABC --options ../convert.xml
convert_potential gromacs

convert.xml:
<cg>
<bonded>
<name>AB</name>
<inverse>
<gromacs>
<table>../tables/table_b0.xvg</table>
</gromacs>
</inverse>
</bonded>
<bonded>
<name>BC</name>
<inverse>
<gromacs>
<table>../tables/table_b1.xvg</table>
</gromacs>
</inverse>
</bonded>
<angle>
<name>ABC</name>
<inverse>
<gromacs>
<table>../tables/table_a0.xvg</table>
</gromacs>
</inverse>
</angle>

<inverse>
<gromacs>
<table_end>3.0</table_end>
<table_bins>0.002</table_bins>
<pot_max>1000000</pot_max>
</gromacs>
</inverse>
</cg>

Diheral i currently don't have tabulated one (fitted functional form
in my case), but should be similar.

Best,
Victor

2011/6/27 chemistry <donet...@gmail.com>:

[chemistry]

Hello!

Thanks again for advices. It's helped me a lot.
I have already created all files what I need for CG calculation. But
now I have a problem with a tabulated bond interaction. I've checked
already this problem on the gromacs mailing-list. Unfortunately they
do not have any good advice there how to solve this problem. I would
be very grateful if you can give me some advice how to solve it. I
have next error message:

"Fatal error:
A tabulated bond interaction table number 2 is out of the table range:
r 0.646802, between table indices 646 and 647, table length 501"

Thanks a lot in advance,
Sergio.

On Jun 27, 6:33 pm, Victor Ruehle <rue...@votca.org> wrote:
> Hey,
>

> 2011/6/27 chemistry <donets1...@gmail.com>:

> ...
>
> read more »

[Sebastian]

Hi 'chemistry',


it seems your bond is streching to far, this could be due to a too
weak minimum in the bonded interaction or beacause your system
explodes (too high energies) in some other part of the system.
I would try:
1) run a steepest decent before the actual simulation
2) make the bonded table longer by filling up some zeroes. Then check
if something else breaks (with a 'out of range') error....

-Sebastian

> ...
>
> read more »

[chemistry]

Hello!

Seems that I have a problem with my CG-structure. I've got this
structure from all-atom simulation with the help of the csg_map:

$csg_map --top topol.tpr --trj traj.trr --cg mappin.xml --out cg.gro

In the mappin.xml file every monomer of my system (P3HT) divided on
three beads and each bead in my polymer has different name (I have 12
monomers in my polymer-chain).
How exactly did you get the CG-structure for propane in your example?

Thanks a lot in advance,
Sergio

> ...
>
> read more »

[Christoph Junghans]

2011/7/1 chemistry <donet...@gmail.com>:

> Seems that I have a problem with my CG-structure. I've got this
> structure from all-atom simulation with the help of the csg_map:
>
> $csg_map --top topol.tpr --trj traj.trr --cg mappin.xml --out cg.gro
>
> In the mappin.xml file every monomer of my system (P3HT) divided on
> three beads and each bead in my polymer has different name (I have 12
> monomers in my polymer-chain).
> How exactly did you get the CG-structure for propane in your example?

I didn't get what exactly is your question. The above csg_map command
looks correct to me.
View the cg.gro (maybe with VMD) to see if the mapping was done correctly.

To start an ibi simulation you will need:
-initial configuration (your cg.gro) - make sure that
cg.inverse.gromacs.conf in your option xml file has the same value, as
'conf.gro' is the default name.
-gromacs run parameter file (grompp.mdp)
-gromacs text topology (topol.top) - output of csg_gmxtopol can be
used a starting point
-gromacs index file (index.ndx) - run make_ndx on cg initial configuration
-target distributions (filenames inverse.target inside the interaction
block) in the xml setting file
-any additional files (bonded tables, table.xvg) to make gromacs happy
- add them to inverse.filelist

For details please have a look at the manual:
<http://votca.googlecode.com/files/votca-manual-1.2.pdf>

Cheers,

Christoph

> --
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>
>

--

[chemistry]

Hello!

Seems that I have not a good initial CG-structure. I've got it with
the help of csg_map:

$csg_map --top topol.tpr --trj traj.trr --cg mappin.xml --out cg.gro

In my mappin.xml file every monomer of my system (P3HT) divided on the
three beads and each bead has a different name.
How exactly did you get initial CG-structure for propene in your
example?

Thanks a lot in advance,
Sergio

On Jun 30, 12:20 pm, Sebastian <frit...@mpip-mainz.mpg.de> wrote:

> ...
>
> read more »

[chemistry]

Sorry, it was a problem with the internet and that's why I posted the
same message twice.

I'm doing it in the same way how you wrote. So, I'll check all stuff
again and thanks for fast answer.

Kind regards.

> ...
>
> read more »

[Victor Ruehle]

Be aware, if you have a bug in your coarse-grained topology, it might
immediately crash the simulations similar to the problem you
described. The csg_map will give a reasonable initial structure, this
should do well if your coarse-grained potentials are ok (eventually do
a steep before). The topology generation (csg_gmxtopol) just provides
a point to start from but will always require tuning by hand to put in
correct parameters.

Also verify your mapping by loading atomistic + coarse-grained
structures in vmd.

2011/7/1 chemistry <donet...@gmail.com>:

[chemistry]

Hey, Victor!

With table_b1.xvg and table_a1.xvg from your tutorial simulation for
propane works well.
I'd tried to process the potentials for propane myself and after when
I started the simulations I've got the same mistake like for my
system:

"Fatal error:
A tabulated bond interaction table number 1 is out of the table range:
r 3.157974, between table indices 3157 and 3158, table length 501"

Seems that I have some problem with creating the tables_*.xvg
Can you please check the way of post-processing of the potentials.
At the beginning I had the same shape of the potential like in your
case (I've got it with csg_boltzmann from all-atom MD simulation of
propane at T=200 K):

bond:

sed -e '1,5d' -e 's/$/ i/' AB.pot | tac | sed -e '1,4d' | tac > AB.cut

csg_call table smooth AB.cut AB.smooth
csg_resample --in AB.smooth --out AB.refined --grid 0::0.001:0.5
csg_call table extrapolate --function quadratic AB.refined AB.pot.cur

csg_call --options table.xml convert_potential xvg --type bonded
AB.pot.cur table_b1.xvg

where table.xml:

<cg>
<inverse>
<gromacs>
<pot_max>1e8</pot_max>
<table_end>0.5</table_end>

<table_bins>0.002</table_bins>
</gromacs>
</inverse>
</cg>

angle:

sed -e 's/$/ i/' ABA_angle.pot | tac | sed -e '1,2d' | tac > ABA.cut
awk '{print $1/3.141592654*180.0,$2,$3,$4}' ABA.cut > ABA.new.cut
csg_call table smooth ABA.new.cut ABA.smooth
csg_resample --in ABA.smooth --out ABA.refined --grid 0::0.05:180
csg_call table extrapolate --function quadratic ABA.refined
ABA.pot.cur
csg_call --options table.xml convert_potential xvg --type bonded
ABA.pot.cur table_a1.xvg

where table.xml:

<cg>
<inverse>
<gromacs>
<pot_max>1e8</pot_max>
<table_end>180</table_end>
<table_bins>0.05</table_bins>
</gromacs>
</inverse>
</cg>

In both cases the potentials look similar around the minimum, but
afterwords they are totally different. I wanted to get the same
table_*.xvg like in your example.

Yours respectfully,
Sergio

On Jul 1, 11:34 am, Victor Ruehle <rue...@votca.org> wrote:
> Be aware, if you have a bug in your coarse-grained topology, it might
> immediately crash the simulations similar to the problem you
> described. The csg_map will give a reasonable initial structure, this
> should do well if your coarse-grained potentials are ok (eventually do
> a steep before). The topology generation (csg_gmxtopol) just provides
> a point to start from but will always require tuning by hand to put in
> correct parameters.
>
> Also verify your mapping by loading atomistic + coarse-grained
> structures in vmd.
>

> 2011/7/1 chemistry <donets1...@gmail.com>:

> ...
>
> read more »

[Victor Ruehle]

Hey,

can you please attach your table_?.xvg

Cheers,
Victor

2011/7/4 chemistry <donet...@gmail.com>:

[chemistry]

Hey,

the format of the table_*.xvg which was created after post-processing
looks like this:

table_a1.xvg:

0.0000000000e+00 8.6955642509e+07 0.0000000000e+00
5.0000000000e-02 8.6862417509e+07 1.8640000000e+06
1.0000000000e-01 8.6769242509e+07 1.8630000000e+06
1.5000000000e-01 8.6676117509e+07 1.8620000000e+06
2.0000000000e-01 8.6583042509e+07 1.8610000000e+06

and yesterday I've created the same format of the table like in your
case by myself. I used for this C-programing and described the
potential with the help of harmonic potential. And now it works well.

new one table_a1.xvg:

0.000000 1201.461834 0
0.050000 1200.343519 0
0.100000 1199.225724 0
0.150000 1198.108451 0
0.200000 1196.991698 0

In both cases the potentials look similar around the minimum. Is it
possible that the GROMACS in someway cannot read correctly the
table_*.xvg?

Kind regards,
Sergio

On Jul 4, 7:50 pm, Victor Ruehle <rue...@votca.org> wrote:
> Hey,
>

> can you please attach your table_?.xvg
>
> Cheers,
> Victor
>

> 2011/7/4 chemistry <donets1...@gmail.com>:

> ...
>
> read more »

[Victor Ruehle]

Hey,

1) I recommend to use version 1.2. The functionality + arguments of
convert_potentials have slightly changed.

2) in the files you sent me, the bad sampled regions were not cut and
therefore the extrapolate failed (zoom in at table_a0.xvg where the
extrapolated region at the left starts). This will lead to a very
strong peak in the force and is probably what messes up your run.
Please make sure to really cut the very rough points at the left and
right of bonded potentials. This was done in the sed commands i send
you. Either adjust the number of points there or better skip this
command and do it manually.

Victor

2011/7/5 chemistry <donet...@gmail.com>:

[chemistry]

Hello, Victor!

Is it possible do not use tables_*.xvg and instead of it set the
parameters for bond, angle and dihedral to the topol.top with
equilibrium bond length, angle and force constants. In this case ibi-
procedure for my system works.
And how one can choose the exact simulation time for one iteration for
different systems?

Thanks a lot in advance,
Sergio

On Jul 5, 5:04 pm, Victor Ruehle <rue...@votca.org> wrote:
> Hey,
>

> 1) I recommend to use version 1.2. The functionality + arguments of
> convert_potentials have slightly changed.
>
> 2) in the files you sent me, the bad sampled regions were not cut and
> therefore the extrapolate failed (zoom in at table_a0.xvg where the
> extrapolated region at the left starts). This will lead to a very
> strong peak in the force and is probably what messes up your run.
> Please make sure to really cut the very rough points at the left and
> right of bonded potentials. This was done in the sed commands i send
> you. Either adjust the number of points there or better skip this
> command and do it manually.
>
> Victor
>

> 2011/7/5 chemistry <donets1...@gmail.com>:

> ...
>
> read more »

[Christoph Junghans]

2011/7/7 chemistry <donet...@gmail.com>:

> Is it possible do not use tables_*.xvg and instead of it set the
> parameters for bond, angle and dihedral to the topol.top with
> equilibrium bond length, angle and force constants. In this case ibi-
> procedure for my system works.

Yes, if the potential can be reasonably approximated by a harmonic
form. Just compare the table to k/2*(r-r_0)^2 !

> And how one can choose the exact simulation time for one iteration for
> different systems?

There is no rule. The iteration has to be long enough, so that the
distributions of the interactions, you want to iteratively refine, are
sampled reasonable. Too long iterations just waste your computer time
;-)
I usually do 100 short iterations follow by 50 longer ones, but that
is my personal recipe.

Cheers,

Christoph

> --
> You received this message because you are subscribed to the Google Groups "votca" group.
> To post to this group, send email to vo...@googlegroups.com.
> To unsubscribe from this group, send email to votca+un...@googlegroups.com.
> For more options, visit this group at http://groups.google.com/group/votca?hl=en.
>
>

--

[chemistry]

Hello!

in U(n+1) = U(n) + ai*kb*T*ln(P(n)/P(ref)) where one can set numerical
factor ai (0<ai<1). At the moment my calculation is diverges, so in
general how one can reach better convergency?

Kind regards,
Sergio

On Jul 7, 5:03 pm, Christoph Junghans <jungh...@votca.org> wrote:
> 2011/7/7 chemistry <donets1...@gmail.com>:> Is it possible do not use tables_*.xvg and instead of it set the

> ...
>
> read more »

[Victor Rühle]

Use the post update script scale and its corresponding option

http://www.votca.org/Documentation/reference-cginteraction
--
Diese Nachricht wurde von meinem Android-Mobiltelefon mit K-9 Mail gesendet.

chemistry <donet...@gmail.com> schrieb:

Hello! in U(n+1) = U(n) + ai*kb*T*ln(P(n)/P(ref)) where one can set numerical factor ai (0<ai<1). At the moment my calculation is diverges, so in general how one can reach better convergency? Kind regards, Sergio On Jul 7, 5:03 pm, Christoph Junghans <jungh...@votca.org> wrote: > 2011/7/7 chemistry <donets1...@gmail.com>:> Is it possible do not use tables_*.xvg and instead of it set the > > parameters for bond, angle and dihedral to the topol.top with > > equilibrium bond length, angle and force constants. In this case ibi- > > procedure for my system works. > > Yes, if the potential can be reasonably approximated by a harmonic > form. Just compare the table to k/2*(r-r_0)^2 ! > > > And how one can choose the exact simulation time for one iteration for > > different systems? > > There is no rule. The iteration has to be long enough, so that the > distributions of the interactions, you want to iteratively refine, are > sampled reasonable. Too long iterations just waste your computer time > ;-) > I usually do 100 short iterations follow by 50 longer ones, but that > is my personal recipe. > > Cheers, > > Christoph > > > > > Thanks a lot in advance, > > Sergio > > > On Jul 5, 5:04 pm, Victor Ruehle <rue...@votca.org> wrote: > >> Hey, > > >> 1) I recommend to use version 1.2. The functionality + arguments of > >> convert_potentials have slightly changed. > > >> 2) in the files you sent me, the bad sampled regions were not cut and > >> therefore the extrapolate failed (zoom in at table_a0.xvg where the > >> extrapolated region at the left starts). This will lead to a very > >> strong peak in the force and is probably what messes up your run. > >> Please make sure to really cut the very rough points at the left and > >> right of bonded potentials. This was done in the sed commands i send > >> you. Either adjust the number of points there or better skip this > >> command and do it manually. > > >> Victor > > >> 2011/7/5 chemistry <donets1...@gmail.com>: > > >> > Hey, > > >> > the format of the table_*.xvg which was created after post-processing > >> > looks like this: > > >> > table_a1.xvg: > > >> > 0.0000000000e+00   8.6955642509e+07 0.0000000000e+00 > >> > 5.0000000000e-02   8.6862417509e+07 1.8640000000e+06 > >> > 1.0000000000e-01   8.6769242509e+07 1.8630000000e+06 > >> > 1.5000000000e-01   8.6676117509e+07 1.8620000000e+06 > >> > 2.0000000000e-01   8.6583042509e+07 1.8610000000e+06 > > >> > and yesterday I've created the same format of the table like in your > >> > case by myself. I used for this C-programing and described the > >> > potential with the help of harmonic potential. And now it works well. > > >> > new one table_a1.xvg: > > >> > 0.000000 1201.461834 0 > >> > 0.050000 1200.343519 0 > >> > 0.100000 1199.225724 0 > >> > 0.150000 1198.108451 0 > >> > 0.200000 1196.991698 0 > > >> > In both cases the potentials look similar around the minimum. Is it > >> > possible that the GROMACS in someway cannot read correctly the > >> > table_*.xvg? > > >> > Kind regards, > >> > Sergio > > >> > On Jul 4, 7:50 pm, Victor Ruehle <rue...@votca.org> wrote: > >> >> Hey, > > >> >> can you please attach your table_?.xvg > > >> >> Cheers, > >> >> Victor > > >> >> 2011/7/4 chemistry <donets1...@gmail.com>: > > >> >> > Hey, Victor! > > >> >> > With table_b1.xvg and table_a1.xvg from your tutorial simulation for > >> >> > propane works well. > >> >> > I'd tried to process the potentials for propane myself and after when > >> >> > I started the simulations I've got the same mistake like for my > >> >> > system: > > >> >> > "Fatal error: > >> >> > A tabulated bond interaction table number 1 is out of the table range: > >> >> > r 3.157974, between table indices 3157 and 3158, table length 501" > > >> >> > Seems that I have some problem with creating the tables_*.xvg > >> >> > Can you please check the way of post-processing of the potentials. > >> >> > At the beginning I had the same shape of the potential like in your > >> >> > case (I've got it with csg_boltzmann from all-atom MD simulation of > >> >> > propane at T=200 K): > > >> >> > bond: > > >> >> > sed -e '1,5d' -e 's/$/ i/' AB.pot | tac | sed -e '1,4d' | tac > AB.cut > >> >> > csg_call table smooth AB.cut AB.smooth > >> >> > csg_resample --in AB.smooth --out AB.refined --grid 0::0.001:0.5 > >> >> > csg_call table extrapolate --function quadratic AB.refined AB.pot.cur > >> >> > csg_call --options table.xml convert_potential xvg --type bonded > >> >> > AB.pot.cur table_b1.xvg > > >> >> > where table.xml: > > >> >> > <cg> > >> >> >   <inverse> > >> >> >    <gromacs> > >> >> >     <pot_max>1e8</pot_max> > >> >> >     <table_end>0.5</table_end> > >> >> >     <table_bins>0.002</table_bins> > >> >> >    </gromacs> > >> >> >   </inverse> > >> >> > </cg> > > >> >> > angle: > > >> >> > sed -e 's/$/ i/' ABA_angle.pot | tac | sed -e '1,2d' | tac  > ABA.cut > >> >> > awk '{print $1/3.141592654*180.0,$2,$3,$4}' ABA.cut > ABA.new.cut > >> >> > csg_call table smooth ABA.new.cut ABA.smooth > >> >> > csg_resample --in ABA.smooth --out ABA.refined --grid 0::0.05:180 > >> >> > csg_call table extrapolate --function quadratic ABA.refined > >> >> > ABA.pot.cur > >> >> > csg_call --options table.xml convert_potential xvg --type bonded > >> >> > ABA.pot.cur table_a1.xvg > > >> >> > where table.xml: > > >> >> > <cg> > >> >> >   <inverse> > >> >> >    <gromacs> > >> >> >     <pot_max>1e8</pot_max> > >> >> >     <table_end>180</table_end> > >> >> >     <table_bins>0.05</table_bins> > >> >> >    </gromacs> > >> >> >   </inverse> > >> >> > </cg> > > >> >> > In both cases the potentials look similar around the minimum, but > >> >> > afterwords they are totally different. I wanted to get the same > >> >> > table_*.xvg like in your example. > > >> >> > Yours respectfully, > >> >> > Sergio > > >> >> > On Jul 1, 11:34 am, Victor Ruehle <rue...@votca.org> wrote: > >> >> >> Be aware, if you have a bug in your coarse-grained topology, it might > >> >> >> immediately crash the simulations similar to the problem you > >> >> >> described. The csg_map will give a reasonable initial structure, this > >> >> >> should do well if your coarse-grained potentials are ok (eventually do > >> >> >> a steep before). The topology generation (csg_gmxtopol) just provides > >> >> >> a point to start from but will always require tuning by hand to put in > >> >> >> correct parameters. > > >> >> >> Also verify your mapping by loading atomistic + coarse-grained > >> >> >> structures in vmd. > > >> >> >> 2011/7/1 chemistry <donets1...@gmail.com>: > > >> >> >> > Sorry, it was a problem with the internet and that's why I posted the > >> >> >> > same message twice. > > >> >> >> > I'm doing it in the same way how you wrote. So, I'll check all stuff > >> >> >> > again and thanks for fast answer. > > >> >> >> > Kind regards. > > >> >> >> > On Jul 1, 11:14 am, chemistry <donets1...@gmail.com> wrote: > >> >> >> >> Hello! > > >> >> >> >> Seems that I have not a good initial CG-structure. I've got it with > >> >> >> >> the help of csg_map: > > >> >> >> >> $csg_map --top topol.tpr --trj traj.trr --cg mappin.xml --out cg.gro > > >> >> >> >> In my mappin.xml file every monomer of my system (P3HT) divided on the > >> >> >> >> three beads and each bead has a different name. > >> >> >> >> How exactly did you get initial CG-structure for propene in your > >> >> >> >> example? > > >> >> >> >> Thanks a lot in advance, > >> >> >> >> Sergio > > >> >> >> >> On Jun 30, 12:20 pm, Sebastian <frit...@mpip-mainz.mpg.de> wrote: > > >> >> >> >> > Hi 'chemistry', > > >> >> >> >> > it seems your bond is streching to far, this could be due to a too > >> >> >> >> > weak minimum in the bonded interaction or beacause your system > >> >> >> >> > explodes (too high energies) in some other part of the system. > >> >> >> >> > I would try: > >> >> >> >> > 1) run a steepest decent before the actual simulation > >> >> >> >> > 2) make the bonded table longer by filling up some zeroes. Then check > >> >> >> >> > if something else breaks (with a 'out of range') error.... > > >> >> >> >> > -Sebastian > > >> >> >> >> > On Jun 30, 10:34 am, chemistry <donets1...@gmail.com> wrote: > > >> >> >> >> > > Hello! > > >> >> >> >> > > Thanks again for advices. It's helped me a lot. > >> >> >> >> > > I have already created all files what I need for CG calculation. But > >> >> >> >> > > now I have a problem with a tabulated bond interaction. I've checked > >> >> >> >> > > already this problem on the gromacs mailing-list. Unfortunately they > >> >> >> >> > > do not have any good advice there how to solve this problem. I would > >> >> >> >> > > be very grateful if you can give me some advice how to solve it. I > >> >> >> >> > > have next error message: > > >> >> >> >> > > "Fatal error: > >> >> >> >> > > A tabulated bond interaction table number 2 is out of the table range: > >> >> >> >> > > r 0.646802, between table indices 646 and 647, table length 501" > > >> >> >> >> > > Thanks a lot in advance, > >> >> >> >> > > Sergio. > > >> >> >> >> > > On Jun 27, 6:33 pm, Victor Ruehle <rue...@votca.org> wrote: > > >> >> >> >> > > > Hey, > > >> >> >> >> > > > i also use csg_boltzmann, the tab command (dont forget tab set scale > >> >> >> >> > > > bond / tab set scale angle for bond/angles). some of my examples (the > >> >> >> >> > > > .pot files are the output of csg_boltzmann): > >> >> >> >> > > > bonds: > >> >> >> >> > > > cp ../../pot/AB_bond.pot . > >> >> >> >> > > > sed -e '1,5d' -e 's/$/ i/' AB_bond.pot | tac | sed -e '1,4d' | tac > > >> >> >> >> > > > AB.cut   ; cut bad sampled regions at the boundaries > >> >> >> >> > > > csg_call table smooth AB.cut AB.smooth > >> >> >> >> > > > csg_resample --in AB.smooth --out AB.refined --grid 0::0.001:0.5 > >> >> >> >> > > > csg_call table extrapolate --function quadratic AB.refined AB.pot.cur > >> >> >> >> > > > csg_call --ia-type bonded --ia-name AB --options ../convert.xml > >> >> >> >> > > > convert_potential gromacs > > >> >> >> >> > > > angles: > >> >> >> >> > > > cp ../../pot/ABC_angle.pot . > >> >> >> >> > > > #sed -e '1,3d' -e 's/$/ i/' ABC_angle.pot | tac | sed -e '1,3d' | tac > ABC.cut > >> >> >> >> > > > sed -e 's/$/ i/' ABC_angle.pot | tac | sed -e '1,2d' | tac  > ABC.cut > >> >> >> >> > > > csg_call table smooth ABC.cut ABC.smooth > >> >> >> >> > > > csg_resample --in ABC.smooth --out ABC.refined --grid 0::0.001:3.141592654 > >> >> >> >> > > > csg_call table extrapolate --function quadratic --region left > >> >> >> >> > > > ABC.refined ABC.refined > >> >> >> >> > > > csg_call table extrapolate --function > > ... > > read more » -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to vo...@googlegroups.com. To unsubscribe from this group, send email to votca+un...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/votca?hl=en.

[chemistry]

Hey!

Can you please explain how exactly I can set and variate numerical
factor ai (0<ai<1) for U(n+1) = U(n) + ai*kb*T*ln(P(n)/P(ref)).
Because after 10 iteration instead of convergence I have a big
divergence. I've specified already simple pressure correction and it
works:
<cg>
...
<inverse>
<p_target>1</p_target>
<post_update>pressure</post_update>
<post_update_options>
<pressure>
<do>0 0 1</do>
<type>simple</type>
<simple>
<scale>0.0003</scale>
</simple>
</pressure>
</post_update_options>

Which update script I should use for this purpose and in which section
of settings.xml file I need to specify this option?

Thanks a lot in advance,
Sergio.

On Jul 10, 8:12 pm, "Victor Rühle" <rue...@votca.org> wrote:
> Use the post update script scale and its corresponding option
>
> http://www.votca.org/Documentation/reference-cginteraction
> --
> Diese Nachricht wurde von meinem Android-Mobiltelefon mit K-9 Mail gesendet.
>

> chemistry <donets1...@gmail.com> schrieb:

>
> Hello! in U(n+1) = U(n) + ai*kb*T*ln(P(n)/P(ref)) where one can set numerical factor ai (0<ai<1). At the moment my calculation is diverges, so in general how one can reach better convergency? Kind regards, Sergio On Jul 7, 5:03 pm, Christoph Junghans <jungh...@votca.org> wrote: > 2011/7/7 chemistry <donets1...@gmail.com>:> Is it possible do not use tables_*.xvg and instead of it set the > > parameters for bond, angle and dihedral to the topol.top with > > equilibrium bond length, angle and force constants. In this case ibi- > > procedure for my system works. > > Yes, if the potential can be reasonably approximated by a harmonic > form. Just compare the table to k/2*(r-r_0)^2 ! > > > And how one can choose the exact simulation time for one iteration for > > different systems? > > There is no rule. The iteration has to be long enough, so that the > distributions of the interactions, you want to iteratively refine, are > sampled reasonable. Too long iterations just waste your computer
> time > ;-) > I usually do 100 short iterations follow by 50 longer ones, but that > is my personal recipe. > > Cheers, > > Christoph > > > > > Thanks a lot in advance, > > Sergio > > > On Jul 5, 5:04 pm, Victor Ruehle <rue...@votca.org> wrote: > >> Hey, > > >> 1) I recommend to use version 1.2. The functionality + arguments of > >> convert_potentials have slightly changed. > > >> 2) in the files you sent me, the bad sampled regions were not cut and > >> therefore the extrapolate failed (zoom in at table_a0.xvg where the > >> extrapolated region at the left starts). This will lead to a very > >> strong peak in the force and is probably what messes up your run. > >> Please make sure to really cut the very rough points at the left and > >> right of bonded potentials. This was done in the sed commands i send > >> you. Either adjust the number of points there or better skip this > >> command and do it manually. > > >> Victor > > >> 2011/7/5 chemistry <donets1...@gmail.com>: > > >> > Hey,> > >> > the format of the table_*.xvg which was created after post-processing > >> > looks like this: > > >> > table_a1.xvg: > > >> > 0.0000000000e+00   8.6955642509e+07 0.0000000000e+00 > >> > 5.0000000000e-02   8.6862417509e+07 1.8640000000e+06 > >> > 1.0000000000e-01   8.6769242509e+07 1.8630000000e+06 > >> > 1.5000000000e-01   8.6676117509e+07 1.8620000000e+06 > >> > 2.0000000000e-01   8.6583042509e+07 1.8610000000e+06 > > >> > and yesterday I've created the same format of the table like in your > >> > case by myself. I used for this C-programing and described the > >> > potential with the help of harmonic potential. And now it works well. > > >> > new one table_a1.xvg: > > >> > 0.000000 1201.461834 0 > >> > 0.050000 1200.343519 0 > >> > 0.100000 1199.225724 0 > >> > 0.150000 1198.108451 0 > >> > 0.200000 1196.991698 0 > > >> > In both cases the potentials look similar around the minimum. Is it > >> > possible that the GROMACS in someway cannot read correctly the > >> >
>
> table_*.xvg? > > >> > Kind regards, > >> > Sergio > > >> > On Jul 4, 7:50 pm, Victor Ruehle <rue...@votca.org> wrote: > >> >> Hey, > > >> >> can you please attach your table_?.xvg > > >> >> Cheers, > >> >> Victor > > >> >> 2011/7/4 chemistry <donets1...@gmail.com>: > > >> >> > Hey, Victor! > > >> >> > With table_b1.xvg and table_a1.xvg from your tutorial simulation for > >> >> > propane works well. > >> >> > I'd tried to process the potentials for propane myself and after when > >> >> > I started the simulations I've got the same mistake like for my > >> >> > system: > > >> >> > "Fatal error: > >> >> > A tabulated bond interaction table number 1 is out of the table range: > >> >> > r 3.157974, between table indices 3157 and 3158, table length 501" > > >> >> > Seems that I have some problem with creating the tables_*.xvg > >> >> > Can you please check the way of post-processing of the potentials. > >> >> > At the beginning I had the same shape of the potential like in your > >> >> >
> case (I've got it with csg_boltzmann from all-atom MD simulation of > >> >> > propane at T=200 K): > > >> >> > bond: > > >> >> > sed -e '1,5d' -e 's/$/ i/' AB.pot | tac | sed -e '1,4d' | tac > AB.cut > >> >> > csg_call table smooth AB.cut AB.smooth > >> >> > csg_resample --in AB.smooth --out AB.refined --grid 0::0.001:0.5 > >> >> > csg_call table extrapolate --function quadratic AB.refined AB.pot.cur > >> >> > csg_call --options table.xml convert_potential xvg --type bonded > >> >> > AB.pot.cur table_b1.xvg > > >> >> > where table.xml: > > >> >> > <cg> > >> >> >   <inverse> > >> >> >    <gromacs> > >> >> >     <pot_max>1e8</pot_max> > >> >> >     <table_end>0.5</table_end> > >> >> >     <table_bins>0.002</table_bins> > >> >> >    </gromacs> > >> >> >   </inverse> > >> >> > </cg> > > >> >> > angle: > > >> >> > sed -e 's/$/ i/' ABA_angle.pot | tac | sed -e '1,2d' | tac  > ABA.cut > >> >> > awk '{print $1/3.141592654*180.0,$2,$3,$4}' ABA.cut > ABA.new.cut > >> >> > csg_call table
> smooth ABA.new.cut ABA.smooth > >> >> > csg_resample --in ABA.smooth --out ABA.refined --grid 0::0.05:180 > >> >> > csg_call table extrapolate --function quadratic ABA.refined > >> >> > ABA.pot.cur > >> >> > csg_call --options table.xml convert_potential xvg --type bonded > >> >> > ABA.pot.cur table_a1.xvg > > >> >> > where table.xml: > > >> >> > <cg> > >> >> >   <inverse> > >> >> >    <gromacs> > >> >> >     <pot_max>1e8</pot_max> > >> >> >     <table_end>180</table_end> > >> >> >     <table_bins>0.05</table_bins> > >> >> >    </gromacs> > >> >> >   </inverse> > >> >> > </cg> > > >> >> > In both cases the potentials look similar around the minimum, but > >> >> > afterwords they are totally different. I wanted to get the same > >> >> > table_*.xvg like in your example. > > >> >> > Yours respectfully, > >> >> > Sergio > > >> >> > On Jul 1, 11:34 am, Victor Ruehle <rue...@votca.org> wrote: > >> >> >> Be aware, if you have a bug in your coarse-grained topology, it might > >> >> >>
> immediately crash the simulations similar to the problem you > >> >> >> described. The csg_map will give a reasonable initial structure, this > >> >> >> should do well if your coarse-grained potentials are ok (eventually do > >> >> >> a steep before). The topology generation (csg_gmxtopol) just provides > >> >> >> a point to start from but will always require tuning by hand to put in > >> >> >> correct parameters. > > >> >> >> Also verify your mapping by loading atomistic + coarse-grained > >> >> >> structures in vmd. > > >> >> >> 2011/7/1 chemistry <donets1...@gmail.com>: > > >> >> >> > Sorry, it was a problem with the internet and that's why I posted the > >> >> >> > same message twice. > > >> >> >> > I'm doing it in the same way how you wrote. So, I'll check all stuff > >> >> >> > again and thanks for fast answer. > > >> >> >> > Kind regards. > > >> >> >> > On Jul 1, 11:14 am, chemistry <donets1...@gmail.com> wrote: > >> >> >> >> Hello! > > >> >> >> >> Seems that I have not a
> good initial CG-structure. I've got it with > >> >> >> >> the help of csg_map: > > >> >> >> >> $csg_map --top topol.tpr --trj traj.trr --cg mappin.xml --out cg.gro > > >> >> >> >> In my mappin.xml file every monomer of my system (P3HT) divided on the > >> >> >> >> three beads and each bead has a different name. > >> >> >> >> How exactly did you get initial CG-structure for propene in your > >> >> >> >> example? > > >> >> >> >> Thanks a lot in advance, > >> >> >> >> Sergio > > >> >> >> >> On Jun 30, 12:20 pm, Sebastian <frit...@mpip-mainz.mpg.de> wrote: > > >> >> >> >> > Hi 'chemistry', > > >> >> >> >> > it seems your bond is streching to far, this could be due to a too > >> >> >> >> > weak minimum in the bonded interaction or beacause your system > >> >> >> >> > explodes (too high energies) in some other part of the system. > >> >> >> >> > I would try: > >> >> >> >> > 1) run a steepest decent before the actual simulation > >> >> >> >> > 2) make the bonded table longer by filling up
> some zeroes. Then check > >> >> >> >> > if something else breaks (with a 'out of range') error.... > > >> >> >> >> > -Sebastian > > >> >> >> >> > On Jun 30, 10:34 am, chemistry <donets1...@gmail.com> wrote: > > >> >> >> >> > > Hello! > > >> >> >> >> > > Thanks again for advices. It's helped me a lot. > >> >> >> >> > > I have already created all files what I need for CG calculation. But > >> >> >> >> > > now I have a problem with a tabulated bond interaction. I've checked > >> >> >> >> > > already this problem on the gromacs mailing-list. Unfortunately they > >> >> >> >> > > do not have any good advice there how to solve this problem. I would > >> >> >> >> > > be very grateful if you can give me some advice how to solve it. I > >> >> >> >> > > have next error message: > > >> >> >> >> > > "Fatal error: > >> >> >> >> > > A tabulated bond interaction table number 2 is out of the table range: > >> >> >> >> > > r 0.646802, between table indices 646 and 647, table length 501" > > >> >> >>
>
> >> > > Thanks a lot in advance, > >> >> >> >> > > Sergio. > > >> >> >> >> > > On Jun 27, 6:33 pm, Victor Ruehle <rue...@votca.org> wrote: > > >> >> >> >> > > > Hey, > > >> >> >> >> > > > i also use csg_boltzmann, the tab command (dont forget tab set scale > >> >> >> >> > > > bond / tab set scale angle for bond/angles). some of my examples (the > >> >> >> >> > > > .pot files are the output of csg_boltzmann): > >> >> >> >> > > > bonds: > >> >> >> >> > > > cp ../../pot/AB_bond.pot . > >> >> >> >> > > > sed -e '1,5d' -e 's/$/ i/' AB_bond.pot | tac | sed -e '1,4d' | tac > > >> >> >> >> > > > AB.cut   ; cut bad sampled regions at the boundaries > >> >> >> >> > > > csg_call table smooth AB.cut AB.smooth > >> >> >> >> > > > csg_resample --in AB.smooth --out AB.refined --grid 0::0.001:0.5 > >>
>

> ...
>
> read more »

[Christoph Junghans]

You forget adding "scale" to the "post_update" list.

Cheers,

Christoph

2011/7/12 chemistry <donet...@gmail.com>:

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[chemistry]

Hey!

In general i'm trying to reproduce the article ("Coarse-grained
computer simulations of polymer/fullerene bulk heterojunctions for
organic photovoltaic applications", J.Chem.Theory.Comput., Vol.6, No.
2, 2010) to be familiar with the ibi procedure. With the help of VOTCA
I've got all bonded interaction potentials, but i still have a problem
with getting the non-bonded interaction potentials. I have the same
RDFs like in this article. During the first three iterations CG
potentials going down from the initial guess to the desired value, but
after third-fifth iteration it going up and diverge. The scale
parameter seems to be just change how fast or how slow it will
diverge. Is it something else how one can influence on the
convergency?

Thanks a lot in advance,
Sergio

On Jul 12, 5:28 pm, Christoph Junghans <jungh...@votca.org> wrote:
> You forget adding "scale" to the "post_update" list.
>
> Cheers,
>
> Christoph
>

> 2011/7/12 chemistry <donets1...@gmail.com>:

> ...
>
> read more »

[Victor Rühle]

Hey,

Hard to tell what's going wrong, I think you have to play a bit with
it. Maybe first try without pressure correction (remove pressure in
post_update).

cheers,
victor

> > >> good initial CG-structure. I've got it with > >> >> >> >> the help of csg_map: > > >> >> >> >> $csg_map --top topol.tpr --trj traj.trr --cg mappin.xml --out cg.gro > > >> >> >> >> In my mappin.xml file every monomer of my system (P3HT) divided on the > >> >> >> >> three beads and each bead has a different name. > >> >> >> >> How exactly did you get initial CG-structure for propene in your > >> >> >> >> example? > > >> >> >> >> Thanks a lot in advance, > >> >> >> >> Sergio > > >> >> >> >> On Jun 30, 12:20 pm, Sebastian <frit...@mpip-mainz.mpg.de> wrote: > > >> >> >> >> > Hi 'chemistry', > > >> >> >> >> > it seems your bond is streching to far, this could be due to a too > >> >> >> >> > weak minimum in the...
>
> read more »

[chemistry]

Hey,

how one can change, for example, after third iteration the numerical
parameter and start fourth iteration with a new numerical factor.

cheers,
sergii

> ...
>
> read more »

[Dominik Fritz]

Hi Sergio,

have you checked, that you treat intramolecular exclusions in a
consistent way?
When you obtain the reference RDFs, you typically exclude
(intramolecular) pairs of beads, which are interacting via bonded
interactions.
The same exclusions have to be used for the RDFs coming from the
iteration steps; otherwise your potentials will most probably diverge.

Cheers,

Dominik

[chemistry]

Hi,

In my case i have the similar shape of the RDFs coming from the
iterations to the reference RDFs. But the RDFs coming from the
iterations do not converge to the reference RDFs, that's why i want to
try to change the numerical factor (0<ai<1) during the iterations,
maybe it will help to reach needed value of the potential. And back to
my previous question: "how one can change, for example, after third

iteration the numerical parameter and start fourth iteration with a
new numerical factor."

Thanks a lot in advance,
Sergio.

> ...
>
> read more »

[Christoph Junghans]

2011/7/16 chemistry <donet...@gmail.com>:

> Hi,
>
> In my case i have the similar shape of the RDFs coming from the
> iterations to the reference RDFs. But the RDFs coming from the
> iterations do not converge to the reference RDFs, that's why i want to
> try to change the numerical factor (0<ai<1) during the iterations,
> maybe it will help to reach needed value of the potential. And back to
> my previous question: "how one can change, for example, after third
> iteration the numerical parameter and start fourth iteration with a
> new numerical factor."

We do not support something like this.
It is not hard to implement it, but things like this are better done
by hand anyway.

1.) Do 3 iterations
2.) Change the scale factor
3.) Do more iterations

Cheers,

Christoph

[chemistry]

Hello!!!

I've installed VOTCA 1.2 and now it works with the tables for bonds
and angle in case of monomer. But i have another problem, i have three
different beads (A, B and C) and that's why i have 6 non-bonded
interactions. I've checked all target RDFs and i did not see any
artifacts on it. But on the "C-C.pot.new" which used in the first
iteration the potential in the region from 0.33 to 0 instead of
increasing is decreasing and has the value "-4937870000" in zero
point. And another problem that after first iteration on two of my
RDFs (A-A.dist.new and C-C.dist.new) appear strange peaks in region
where probability should be zero. When i'd checked the trajectory
confout.gro i really saw between some of the molecules very short
distances for A-A and C-C. How is it possible if the potential for all
interactions, except C-C.pot.new, very strong on this distances and in
this case the beads should not come so close to each other? And can
you please explain to me to fully understand how exactly gromacs works
with the tables for the non-bonded interactions?

Thanks a lot in advance,
Sergio

On Jul 16, 4:42 pm, Christoph Junghans <jungh...@votca.org> wrote:
> 2011/7/16 chemistry <donets1...@gmail.com>:> Hi,

> ...
>
> read more »

[Christoph Junghans]

2011/8/1 chemistry <donet...@gmail.com>:

> I've installed VOTCA 1.2 and now it works with the tables for bonds
> and angle in case of monomer. But i have another problem, i have three
> different beads (A, B and C) and that's why i have 6 non-bonded
> interactions. I've checked all target RDFs and i did not see any
> artifacts on it. But on the "C-C.pot.new" which used in the first
> iteration the potential in the region from 0.33 to 0 instead of
> increasing is decreasing and has the value "-4937870000" in zero
> point. And another problem that after first iteration on two of my
> RDFs (A-A.dist.new and C-C.dist.new) appear strange peaks in region
> where probability should be zero. When i'd checked the trajectory
> confout.gro i really saw between some of the molecules very short
> distances for A-A and C-C. How is it possible if the potential for all
> interactions, except C-C.pot.new, very strong on this distances and in
> this case the beads should not come so close to each other? And can
> you please explain to me to fully understand how exactly gromacs works
> with the tables for the non-bonded interactions?

It is hard to say what goes wrong, have you installed the VOTCA
version from Mercurial
(using build.sh) ? We recently fixed some small issue in there related
to calculating the initial potential:
<http://code.google.com/p/votca/source/list?repo=csg&r=stable>

However, it seems to me that the automatic extrapolation failed somewhere.
Go to step_000 and have a look at
-NAME.dist.tgt that are the target distributions VOTCA uses
internally, it is a spline interpolated version of the given targets.
-NAME.pot.new that is the k_BT*log(rdf) and then extrapolated
exponentially on the left side and extrapolated constant on the right
side.
If the dist.tgt or pot.new in step_000 look incorrect, you should
check your given target distributions again.
Sometimes it is easier to create an initial guess for the potential by
hand. It can be put in the maindir under the name 'NAME.pot.in'.

If the dist.tgt and pot.new in step_000 look correct, go to step_001
and have a look at:
-NAME.dist.new - the distribution calculated from the simulation,
maybe it is too rough, then you have to increase the length of the
simulation in the mdp file.
-NAME.dpot.new - the potential update calculated from NAME.dist.new
-NAME.pot.new - sum of NAME.pot.cur and NAME.dpot.new

Sometimes it also helps to set 'min' in seetings.xml to a value
unequal 0 (in your case 0.33 or so) to prevent VOTCA from calculating
an update in the region r < min.

Cheers,

Christoph

[Denis Andrienko]

Hi Sergio,

A side remark: IBI is nothing else but a numerical scheme which
converges your CG rdf to the reference one. Nobody ever proved that it
is supposed to converge. In fact people do know that there might be
difficulties in converging to the target rdf for multicomponent
mixtures. Try to use small scaling factors or/and converge rdfs step
by step - first A-A, then B-B, ...

You are entering a user-steered expert-driven part of coarse-graining.
Good luck ;)
Denis