[gmx-users] Re: gmx-users Digest, Vol 42, Issue 50

chiloo Laohpongspaisan chiloo77 at yahoo.com
Sat Oct 13 13:00:30 CEST 2007

Thank you very much, Zhenhei.
Other Mails:
chiloo7 at hotmail.com
chiloo777 at gmail.com

----- Original Message ----
From: Li Zhenhai <shibalagu.thu at gmail.com>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Sent: Saturday, October 13, 2007 5:44:02 PM
Subject: [gmx-users] Re: gmx-users Digest, Vol 42, Issue 50

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" <X.Periole at rug.nl>
Subject: Re: [gmx-users] Calculating the energy of one molecule in the
    multi-molecule system
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <web-56146831 at mail3.rug.nl>
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

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
Tel: 86-10-62773779
E-mail: shibalagu.thu at gmail.com


======= 2007-10-13 18:00:07 您在来信中写道:=======

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>Today's Topics:
>  1. Energy of each composition (chiloo Laohpongspaisan)
>Message: 1
>Date: Sat, 13 Oct 2007 01:02:08 -0700 (PDT)
>From: chiloo Laohpongspaisan <chiloo77 at yahoo.com>
>Subject: [gmx-users] Energy of each composition
>To: gmx-users at gromacs.org
>Message-ID: <943314.93877.qm at web31602.mail.mud.yahoo.com>
>Content-Type: text/plain; charset="us-ascii"
>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, 
>Other Mails:
>chiloo7 at hotmail.com
>chiloo777 at gmail.com
>Pinpoint customers who are looking for what you sell. 
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