[gmx-users] tabulated potential and long range pressure correction

Berk Hess gmx3 at hotmail.com
Tue Dec 4 09:51:33 CET 2007

>From: "Adrien Leygue" <adrien.leygue at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Subject: [gmx-users] tabulated potential and long range pressure correction
>Date: Mon, 3 Dec 2007 18:17:56 +0200
>Dear Gromacs users,
>I am using Gromacs on a system for which I have modified LJ
>interactions which i have to treat using fully tabulated potentials.
>-Electrostatics are handled using PME.
>-I have User for vdwtype in my mdp options, several energy groups and
>matching table_X_Y.xvg  files for the modified Vdw interactions.
>After reading the Gromacs manual I still do not understand if Gromacs
>can compute the long-range (beyond cut-off) dispersion correction for
>pressure and energy when using fully tabulated potentials. If Gromacs
>can do that then how is this implemented from the tabulated potential:
>how far do I have to tabulate, what is the influence of the
>table_extension parameter,....?
>Let's say that my potential between species X and Y is V(r) and the
>columns 4 to 7 of table_X_Y.xvg are: V(r)  V''(r) V(r) V''(r)
>For the non bonded parameters I can use  0 1 or 1 0. But is this
>equivalent for computing the dispersion correction?
>Thanks for your help/comments

With vdwtype=user Gromacs applies exactly the same dispersion correction
as for a plain cut-off. Thus to obtain correct results your C6 parameters
should really be dispersion parameters and your tabulated potential
should be close to r^-6 around the cut-off.

For vdwtype=switch or shift an exact integration is performed to for the
swicthed part. This can also be applied for user potentials by changing
one line in the code.

So it will not work correctly for the example you describe above.


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