From: "merc mertens" <[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] g_energy sum
Date: Mon, 30 Apr 2007 10:00:11 +0200
hello,
you are right but "summing" over 1 term was done only for testing purposes.
first i tried to sum up all lj terms but ran into the same problem.
nevertheless i finally found the reason for the difference. the energy file
is from a rerun. during the setup mdrun complained that not all frames of
the trajectory used for rerunning contained velocities. therefore i reran a
converted trajectory containing only the frames with velocities (i.e. only
every 100th frame). the resulting energy.xvg contained 21 energy values but
the sum was averaged over 2000001 steps (see below). this explains the
small average value from "-sum".
this leads to the next question: was it wrong to only use the frames
containing velocities in the rerun??
thanks for the help and suggestions,
merc
Ah, that explains it indeed.
Unfortunately mdrun -rerun produces incorrect averages and fluctuations
in the energy file when you do not use EVERY frame.
I think this problem is currently not documented.
Only using every frame (nstxout=1 for the original run) will solve this
problem.
But anyhow, your average from the xvg file is fine and accurate.
For energies you can use all frames, not only the ones with velocities.
Only the kinetic energy and the virial are affected by the velocities.
Berk.
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