From: "Jones de Andrade" <[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] how to remove an energy contribution in gromacs?
Date: Mon, 6 Aug 2007 09:49:26 -0300
Hi all.
Well, I'm trying to calculate an <E> energy from my simulations, where <E>
here stands only for the sum of *intermolecular* vdw and coulombic terms,
and LJ(1-4) and coul(1-4). This means that I should find a way to exclude
any "1-5", "1-6", "1-7" and so on contributions for coulombic and vdw
energies, which I guess are included in the SR terms if the rcut is long
enough.
I though on doing it by use of a modified topology (with an arbitrary
increased "nexcl" term) after the simulation is completed just for a
"-rerun" job, and then use the g_energy program to calculate these
contributions.
Unfortunatelly, for some reason I'm not getting the correct values by large
differences. Properly saying, only doing the above described procedure is
yelding me even modifications in the bond, angle and dihedral terms of my
simulations, which should not vary in a rerun with new nexcl values.
Moreover, all energy terms with no exception seem to be only divided by a
factor around 10., in comparison with the simulations with the original
nexcl.
I'm pretty sure I'm missing something here, but I have no idea of what
could
it be. Could someone please help me with this matter somehow?
Thanks a lot in advance.
This seems the right approach to me.
I don't know what you are doing exactly.
But are you aware that the averages in g_energy and in the log file
are using every integration step, whereas with rerun you only get values
for every frame in your trajectory?
I think the averages of mdrun -rerun are still incorrect, you need to use
the average of the values in the energy.xvg file.
Also obtaining accurate potential energy averages for even small systems
requires a LOT of statistics.
Berk.
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