Hello, chiloo,
Professor Xavier Periole told me a method to extract the energy of one
composition.
You can follow what he/she said:
Message: 2
Date: Thu, 11 Oct 2007 14:25:35 +0200
From: "Xavier Periole" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Calculating the energy of one molecule in the
multi-molecule system
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain;charset=utf-8;format="flowed"
To get the bonded energy terms of one molecule in your system you
have to generate a trajectory file containing this molecule only:
trjconv -f full.trr -n molecule.ndx -o molecule.trr
and then rerun the simulation using a tpr containing only the topology
of your molecule:
grompp -f molecule.mdp -c molecule.gro -o molecule.tpr
mdrun -rerun molecule.trr -s molecule.tpr
Notes:
1- you MUST use the a trr trajectory (full precision). the coordinates
in xtc files are not precise enough.
2- the molecule.mdp should be identical to the original one except
for the update of the neighbor list (nstlist = 1) and print energies
every step (nstenergy).
Li Zhenhai
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
China
Tel: 86-10-62773779
E-mail: [EMAIL PROTECTED]
2007-10-13
======= 2007-10-13 18:00:07 您在来信中写道：=======
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> 1. Energy of each composition (chiloo Laohpongspaisan)
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>----------------------------------------------------------------------
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>Message: 1
>Date: Sat, 13 Oct 2007 01:02:08 -0700 (PDT)
>From: chiloo Laohpongspaisan <[EMAIL PROTECTED]>
>Subject: [gmx-users] Energy of each composition
>To: gmx-users@gromacs.org
>Message-ID: <[EMAIL PROTECTED]>
>Content-Type: text/plain; charset="us-ascii"
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>Dear all,
>
>Is there a tool of Gromacs extracing the energy of some composition in the
>system?
>For example, there are protein, lipid , and water in my system, how can i
>investigate the energy of protein along the time?
>
>Thanks in advance,
>chiloo
>
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