Creating new lammps tutorial

[Scott Sides]

Christoph,

   I'd like to run the propane example with lammps (I've managed to get the spce example running and its very informative).

I've looked at the lammpsreader.cc page you've listed in other posts. I was wondering if you could give a quick outline of steps

needed to bring the propane example up to speed with lammps.

thanks,

Scott W Sides (NREL)

[Christoph Junghans]

2013/9/18 Scott Sides <scott...@gmail.com>:

Start from the gromacs inputs (propane/ibi).
Besides the lammps input files, you will need a topology.xml like this:
<topology base="conf.gro">
<box xx="4.96337" yy="5.13917" zz="4.52386"/>
<molecules>
<clear/>
<define name="Protein" first="1" nbeads="3" nmols="1000"/>
</molecules>
<beadtypes>
<rename name="A1" newname="A"/>
<rename name="A2" newname="A"/>
<rename name="B1" newname="B"/>
<mass name="A" value="15.035"/>
<mass name="B" value="14.027"/>
</beadtypes>
</topology>

The <beadtypes> block is not 100% necessary. Instead of renaming the
beads you could also change the settings.xml file using type "A*"
instead of "A" and "B*" instead of "B" in the type file of the
different interactions.
Correct mass values are not needed for IBI, but lets do it right, so
that we don't forget it later.

Cheers,

Christoph

>
>
> thanks,
> Scott W Sides (NREL)
>

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--
Christoph Junghans
Web: http://www.compphys.de

[Scott Sides]

Ok, I'll get on that.  Couple of questions first

I'm working from the manual for votca 1.2.3 and some of the commands arent working for the propane

tutorial. For example

 csg_gmxtopol --top topol.tpr --cg propane.xml --out out.top

Isnt working for me. For one thing... I dont see a topol.tpr file. When I try

stc-24459s:single_chain ssides$ csg_dump --top topol.top

an error occurred:

input format not supported: topol.top

is the result. The topol.top file is the cloest thing to a topology file that the manual refers to.

Thanks,

Scott

[Chandan Choudhury]

Hi Scott,

The --top  flag takes tpr file as an input.

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA

[Scott W Sides]

Indeed it does. However there is no such file in the tutorial. 

Sent from my iPhone so likely very brief

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[Chandan Choudhury]

On Thu, Sep 19, 2013 at 10:07 AM, Scott W Sides <scott...@gmail.com> wrote:

Indeed it does. However there is no such file in the tutorial.

Dear Scott, 

The tpr file can be generated using the grompp executable of gromacs. It takes the input as structure (pdb/gro) file, topology file (topol.top) and index.ndx file. These files are available in the propane/ibi tutorial

Chandan

Research Fellow

National Chemical Laboratory

India

[Christoph Junghans]

2013/9/18 Scott Sides <scott...@gmail.com>:

> Ok, I'll get on that. Couple of questions first
>
> I'm working from the manual for votca 1.2.3 and some of the commands arent
> working for the propane
> tutorial. For example
>
> csg_gmxtopol --top topol.tpr --cg propane.xml --out out.top
>
>
> Isnt working for me. For one thing... I dont see a topol.tpr file. When I
> try
>
>
> stc-24459s:single_chain ssides$ csg_dump --top topol.top
>
> an error occurred:
>
> input format not supported: topol.top
>
>
> is the result. The topol.top file is the cloest thing to a topology file
> that the manual refers to.

Sorry, I wasn't really clear yesterday about how to get theLAMMPS input files.
csg_gmxtopol will not be really helpful for that as it create a
coarse-grained gromacs (gmx) topology.

Anyhow for LAMMPS you will need:
- data file, easiest is to convert the gro file
$ awk '(NR>2){print $4,$5,$6}' spce.gro
will give you the coordniates to start with.
- lammps script, that is a bit more tricky, easiest will be to start
from spce/ibi_lammps/spce.in and change pair_styles
- topol.xml - see my previous email
- settings.xml - use the on of the gromacs example and add the lammps
options from spce/ibi_lammps
- bonded interactions, you will need to convert table_[ab]1.xvg to the
format of tabulated bonds and angle in lammps.

Hope that helps to get started,

Christoph

>
>
> Thanks,
>
> Scott
>
>
> On Wednesday, September 18, 2013 2:46:14 PM UTC-6, Scott Sides wrote:
>>
>> Christoph,
>>
>> I'd like to run the propane example with lammps (I've managed to get
>> the spce example running and its very informative).
>> I've looked at the lammpsreader.cc page you've listed in other posts. I
>> was wondering if you could give a quick outline of steps
>> needed to bring the propane example up to speed with lammps.
>>
>>
>> thanks,
>> Scott W Sides (NREL)
>>

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[Vitalie Botan]

Dear all,

I am trying to run ibi_lammps tutorial, but the script throws the following error:

ERROR:                                                                  

source_wrapper: Could not get any script from tags 'functions' 'lammps'

Do you have any clues what does it mean?

Googled for this error, but unfortunately without success.

Votca was installed from the opensuse Education repository and a serial lammps version is in the /usr/local/bin folder.

Best,

Vitalie

[Christoph Junghans]

Hi,

2014-06-04 7:14 GMT-06:00 Vitalie Botan <vitali...@gmail.com>:
> Dear all,
>
> I am trying to run ibi_lammps tutorial, but the script throws the following
> error:
>
> ERROR:
> source_wrapper: Could not get any script from tags 'functions' 'lammps'
>
> Do you have any clues what does it mean?
> Googled for this error, but unfortunately without success.
> Votca was installed from the opensuse Education repository and a serial
> lammps version is in the /usr/local/bin folder.

Basically it means the above version of VOTCA doesn't support LAMMPS
as a simulation back-end.
The VOTCA version on OpenSuse Education is 1.2.3, but you will need
1.3-dev to work with LAMMPS:
<https://code.google.com/p/votca/wiki/Installing#Development_Version>

Cheers,

Christoph

> Best,
> Vitalie
>
> On Wednesday, September 18, 2013 10:46:14 PM UTC+2, Scott Sides wrote:
>>
>> Christoph,
>>
>> I'd like to run the propane example with lammps (I've managed to get
>> the spce example running and its very informative).
>> I've looked at the lammpsreader.cc page you've listed in other posts. I
>> was wondering if you could give a quick outline of steps
>> needed to bring the propane example up to speed with lammps.
>>
>>
>> thanks,
>> Scott W Sides (NREL)
>>

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[Vitalie Botan]

Hi Christoph,

Thanks for your reply, although I got to follow it only now (vacation time, sorry), it worked with the dev version of VOTCA. Anyway, I have another problem: on the 2nd iteration step of the SPCE tutorial lammps quits with the following error:

ERROR on proc 0: Pair distance < table inner cutoff (../pair_table_omp.cpp:129)

Callstack:
/opt/votca/share/votca/scripts/inverse/inverse.sh - linenumber 243
    do_external - linenumber 175 in /opt/votca/share/votca/scripts/inverse/functions_common.sh
        /opt/votca/share/votca/scripts/inverse/run_genericsim.sh - linenumber 47
            critical - linenumber 4 (see 'csg_call --cat function critical')
                die - linenumber 2 (see 'csg_call --cat function die')

I have decreased the table_begin value to 0.10 and table_bins to 0.001 in the settings xml in order to start IBI, but it failed again with exactly the same error, now on the step 23. Any ideas?

Best,
Vitalie

[Vitalie Botan]

UPD: with the newest version of tutorial and dump format instead of xyz it works! So please disregard the question above.

[Tonalli Rodríguez]

Hello everyone,

I just want to share my lammps version of the propane/ibi tutorial. I would really appreciate any feedback you can give.

Tonalli

[Sikandar Mashayak]

Thanks Tonali for sharing the files. We will test and let you know.

Thanks,

Sikandar

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