[gmx-users] Tabulated potentials

Martin Vartorelli mrvartorelli at gmail.com
Tue Apr 20 19:38:57 CEST 2010

Hi Gromacs users,

previously I've posted my situation with a simulation and I'm still confused:

I have 3 groups of different atoms: A, B and C, and tabulated bonding
and non-bonding potentials.

The tabulated bonded potentials are specified in the files:


Because the systems is simply this molecule: A--(B)n--C, the *.mdp
file contains the following:

coulombtype = user
vdw-type    = user
energygrps      = A B C
energygrp_table = A B  A C  B B  B C

>From the manual and tutorials I understand that, for the non bonding
part of U, I can suply a file  called "table.xvg" that contains the 7
non-zero columns for r, f, f', g, g', h and h'. The file "table.xvg"
must contain the functions for AB interactions and the remaining
interactions must be in the files "table_A_C.xvg", "table_B_B.xvg" and

So, in the command line I can write: mdrun .... -table table.xvg -tableb table

I'm right?

As a test I have also included the file "table_A_B.xvg" (the same
potential functions that "table.xvg") in the same directory, and when
I look at the log file it shows that this file is readed too. I'm
still unclear... how must I specify the files in an univocal way for
the non bonding interactions that I want?

Gromacs version: 4.0.7

Any help will be appreciated.


PD: I've received some private e-mails explaining to me some issues
about spam, mailing lists, private mails, etc. Thanks to all and I
apologize if I've bother someone, it wasn't my intention. And for
those who spontaneously shows me their support, I don't want it and I
don't need it!

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