From: "Adrien Leygue" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: "Discussion list for GROMACS users" <gmx-users@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
Adrien.
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.
Berk.
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