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: Re: [gmx-users] how to remove an energy contribution in gromacs?
Date: Mon, 6 Aug 2007 11:40:13 -0300
@Xavier:
So, this means:
nstxtcout from 10 to 1
nsteps from 100000 to 10000
nstlog from 10 to 1
nstenergy from 10 to 1
nstlist from 5 to 1.
This is what should be changed in the .mdp file in order to get a proper
rerun g_energy analysis?
@Berk: Thanks a lot for the clarification. But still could not understand
why there is any need for using g_analyze. Could you ple clarify this point
out for me?
In the energy (.edr) file there are three terms for each component in each
frame:
the instantaneous energy, a cumulative sum and a cumulative sum of squares.
g_energy uses the sum term to determine exact averages over the run, not
only modulo nstener frames.
The mdrun -rerun is a bit of a "dirty" hack, so the sum term is only updated
by the frames you rerun, whereas the step count is read from the -rerun
file. So the sum terms and therefore the averages in the log and energy file
are incorrect with -rerun (unless you use nstxout=1 for the original run).
You need to extract the instantaneous values with g_energy and determine
the averages from those.
Additionally you should indeed set nstlist to 1 for the rerun
(although you might have used nstlist=10 for the rerun and nstxout=10
for the original run which is still correct then).
Berk.
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