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

Martin Vartorelli mrvartorelli at gmail.com
Mon Apr 19 15:05:59 CEST 2010

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.


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:


And in the mdrun commandline I'm using the option -tableb table.
But how to handle the non bonding table files?


Must I write

energygrps      = A B C
energygrp_table = AC BB BC

in the mdp file and use the tables


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,
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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