[gmx-users] Tabulated potentials

Gareth Tribello gareth.tribello at gmail.com
Tue Apr 20 20:27:08 CEST 2010


I think this is what you need to do:

(1) Ensure that the topol.top and index.ndx files are set up in the manner
described on the wikki.

(2) Put in the mdp file the following:

energygrps      = A B C
energygrp_table = A C  B B  B C

(3) Now create a set of files as follows

table.xvg - containing the A B interactions
table_A_C.xvg - containing the A C interactions
table_B_B.xvg - containing the B B interactions
table_B_C.xvg - containing the B C interactions

You now run with

mdrun -table table.xvg

gromacs will read in all these files as energygrp_table tells it that it
must read table_A_C.xvg, table_B_B.xvg and table_B_C.xvg as well as

To put this all another way, when you use the command

vdw-type = user

(incidentally I think you said that there are no electrostatics so you can
use coulombtype = cut-off as it will make no difference)

Then you have to provide a table file with definitions of f(r), g(r) and
h(r).  Then gromacs it will use this table for all the non-bonded
interactions (so in your case AA, AB, AC, BB, BC and CC interactions).
 However, when you add:

energygrp_table = A C

Then you are saying, "oh but please do something different for A C
interactions, do what is in the table_A_C.xvg file instead."

As a side note, correct me if I am wrong, but there are no AA or CC
interactions in your molecule?  With the set up I describe above they would
have a functional form equivalent to the A B interaction.  This is obviously
not important if their parameters are equal to zero.

Finally, if your still not sure that stuff has been read in you can look in
the log file, which should say what tables have been read in.  It will also
give you warnings (although these maybe in standard error I can't remember)
if your tables are not set up properly.


On Tue, Apr 20, 2010 at 7:38 PM, Martin Vartorelli
<mrvartorelli at gmail.com>wrote:

> 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:
> table_b1.xvg
> table_a1.xvg
> table_a2.xvg
> table_a3.xvg
> 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
> "table_B_C.xvg".
> 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.
> Martin.
> 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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