[gmx-users] how to remove an energy contribution in gromacs?

[Berk Hess]

>From: "Jones de Andrade" <johannesrs 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: 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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