Tabulated Potential in LAMMPS

[Pratyasha Bhardwaj]

Dear all,

I am trying to run the csg_inverse function for my copolymer system and I was using tabulated potentials for the bonds and angle potentials. I am using Lammps version 2 Aug-2023 and VOTCA version '2021.2'. Does Lammps not support the tabulated potential files of the format 'AA.pot' ? I get the error 'keyword VOTCA' not found. Here are  my scripts as well as the inverse log file. 
An exact harmonic potential wouldn't fit my bond data and my angle correlations are far away from the harmonic curve. I just wanted to know how do I proceed?

Thank You,

Pratyasha

[Pratyasha Bhardwaj]

Here is the correct inverse file. The last one was one of my trials and not the correct one.

[Christoph Junghans]

First of all, VOTCA 2021.2 is old, please update!

Secondly, the error is from "bond_coeff 1 bond1.pot VOTCA #AB" and
bond1.pot is a potential file that you currently don't iterate in
VOTCA, but it is just in the filelist, so VOTCA didn't create it. You
will have to figure out what keyword is used in that file and change
your .in file accordingly.

Christoph

>>
>> Thank You,
>> Pratyasha
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[Pratyasha Bhardwaj]

Ok, thank you for the reply.

No. I created the bond1.pot using csg_boltzmann(and then using the tab option) and using that as my bond potential, so it was created by VOTCA but it is not in the tabular format that lammps read and is not used in the iterations.

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[Christoph Junghans]

On Sun, Dec 8, 2024 at 8:57 AM Pratyasha Bhardwaj
<pratya...@gmail.com> wrote:
>
> Ok, thank you for the reply.
> No. I created the bond1.pot using csg_boltzmann(and then using the tab option) and using that as my bond potential, so it was created by VOTCA but it is not in the tabular format that lammps read and is not used in the iterations.

Did you convert it from VOTCA format to LAMMPS format?
See https://www.votca.org/csg/preparing.html#exporting-the-table
You have to do the same as you do for GROMACS for LAMMPS.
eg. csg_call --options table.xml --ia-type bonded --ia-name XXX
convert_potential lammps table_in.pot table_out.pot

Christoph

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[Pratyasha Bhardwaj]

Thank you so much for your inputs. I was able to start my simulations. I have a few doubts regarding the exclusion list. I used the command 

'csg_dump --top topol.tpr --excl' to get the exclusion list for the atomistic configuration and 'csg_dump --top topol.tpr --cg hexane.xml --excl' for the mapped configuration. As per my understanding the output has all the bonded interactions printed out. For the hexane molecule and the mapped case, the first line represents the bond_angle ABA and hence CG bead 1 has connections with both CG beads 2 and 3. Since bead 2's connection is already mentioned with 1, the second line has just the bond BA connecting cg bead 2 and 3 and so on. 
So, if I have 4 cg beads representing 1 chain, i will have the entry as:

123 #angle

234 #angle

34 #bond

Is my understanding correct?

But what about the first file that doesn't use the mapping scheme(I have attached below). Does it also follow the same logic?

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[Christoph Junghans]

On Thu, Dec 12, 2024 at 3:57 AM Pratyasha Bhardwaj
<pratya...@gmail.com> wrote:
>
> Thank you so much for your inputs. I was able to start my simulations. I have a few doubts regarding the exclusion list. I used the command
> 'csg_dump --top topol.tpr --excl' to get the exclusion list for the atomistic configuration and 'csg_dump --top topol.tpr --cg hexane.xml --excl' for the mapped configuration. As per my understanding the output has all the bonded interactions printed out. For the hexane molecule and the mapped case, the first line represents the bond_angle ABA and hence CG bead 1 has connections with both CG beads 2 and 3. Since bead 2's connection is already mentioned with 1, the second line has just the bond BA connecting cg bead 2 and 3 and so on.
> So, if I have 4 cg beads representing 1 chain, i will have the entry as:
> 123 #angle
> 234 #angle
> 34 #bond
> Is my understanding correct?

The exclusion list are the exclusion pairs and not every pair is
necessarily covered by an interaction.

> But what about the first file that doesn't use the mapping scheme(I have attached below). Does it also follow the same logic?

It is reading the exclusion from the tpr file, you can use gmx dump to
see them too.

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[Pratyasha Bhardwaj]

Dear Christoph,

Although my step 1 starts but I get the error that my bond length exceeds that of the table cutoff. The mentioned bondlength is of the order of box size. My cg structure was generated using the csg_map command and then later modified using vmd topotools. I checked manually, none of the initial bondlengths  are of that order. What could be the possible error that I am making?

I do have another doubt. For the csg_stat command, for all-atomistic data , I used the all-atomistic tpr file with the mapping files, for the cg runs will I need a cg topology file in the xml format?

I am attaching my files : settings.xml used in csg_inverse command, the lammps data file and the script file and the inverse log file.

Thank you,

Pratyasha

[Christoph Junghans]

On Sat, Dec 14, 2024 at 7:37 AM Pratyasha Bhardwaj
<pratya...@gmail.com> wrote:
>
> Dear Christoph,
>
> Although my step 1 starts but I get the error that my bond length exceeds that of the table cutoff. The mentioned bondlength is of the order of box size. My cg structure was generated using the csg_map command and then later modified using vmd topotools. I checked manually, none of the initial bondlengths are of that order. What could be the possible error that I am making?

It is hard to say what went wrong, but bonds can be a bit brittle to
iterate. You could:
a) extend the table and make it is very steep at the end
b) start with harmonic interaction for that bond, get the rest to work
and then put the tabulated interaction back in

> I do have another doubt. For the csg_stat command, for all-atomistic data , I used the all-atomistic tpr file with the mapping files, for the cg runs will I need a cg topology file in the xml format?
> I am attaching my files : settings.xml used in csg_inverse command, the lammps data file and the script file and the inverse log file.

It doesn't matter much what type of topology file you will use as long
as it has all the info you need.
The xml files are useful, if you need to hand tweak the topology.

Christoph

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