[gmx-users] Problem with tabulated potentials for 3 different atoms

[Berk Hess]

Hi,

I don't want to get into discussions on drugs and I don't know if you
already switched package, but I'l post my answer anyhow.

The energy groups in each pair on your energygrp_table line should
be separated by a space.

The table files should contain all columns, unused columns are allowed
to contain zero's, since they are simply ignored.

PS:
Please don't mail me directly with questions on Gromacs,
apart from the good reasons already given on the list,
this is a strong incentive for me not to answer your mail.

Berk

> From: mrvartorelli at gmail.com
> Date: Mon, 19 Apr 2010 10:05:59 -0300
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Problem with tabulated potentials for 3 different atoms
> 
> I'm trying to use tabulated potentials for a very simple system: a
> polymer chain with only 3 kind of atoms: A, B and C, all of it with
> zero charge.
> 
> A--(B)n--C
> 
> The only interactions that accounts are AB, AC, BB and CC, so in my
> mdp file I have writen:
> 
> coulombtype = user
> vdw-type    = user
> energygrps      = A B C
> energygrp_table = AB AC BB BC
> 
> Also, I'm using tabulated bonded potentials for bonds and angles.
> 
> The main questions are how to tell to mdrun that he must read my table
> files and can I be sure that the reading is OK?
> 
> For the bonding part I have the following table files:
> 
> table_b1.xvg
> table_a1.xvg
> table_a2.xvg
> table_a3.xvg
> 
> And in the mdrun commandline I'm using the option -tableb table.
> But how to handle the non bonding table files?
> 
> table_A_B.xvg
> table_A_C.xvg
> table_B_B.xvg
> table_B_C.xvg
> 
> Must I write
> 
> energygrps      = A B C
> energygrp_table = AC BB BC
> 
> in the mdp file and use the tables
> 
> table.xvg
> table_A_C.xvg
> table_B_B.xvg
> table_B_C.xvg
> 
> with the command line for mdrun saying -table table.xvg?
> 
> Another thing, because the tables doesn't have to contain only zero columns...
> Can I put anything on the f and f' columns (because the charge of my
> atoms is zero)?
> Can I put (for example) 0.5 in the g and g' columns and my potential
> (and the force) minus 0.5 in columns h and h'?
> 
> I'm using the 4.0.7 version.
> 
> Again as an abstract:
> 
> System: 1 chain A--(B)n--C
> Bonds: A-B = B-B = B-C --> only one table: table_b1.xvg
> Angles: A-B-B, B-B-B, B-B-C --> 3 tables: table_a1.xvg, table_a2.xvg,
> table_a3.xvg
> Charges: none
> VDW interactions: A-B, A-C, B-B, B-C --> 4 tables table_A_B.xvg,
> table_A_C.xvg, table_B_B.xvg, table_B_C.xvg
> 
> *.mdp lines:
> coulombtype = user
> vdw-type    = user
> energygrps      = A B C
> energygrp_table = ?
> 
> run commandline:
> mdrun -s -c -e -x -g -table ? -tableb ?
> 
> Any help will be appreciated.
> 
> Thank you.
> 
> Martin R. Vartorelli
> -- 
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