[gmx-users] Calculating the energy of one molecule in the

[Li Zhenhai]

Hello, Xavier Periole

    I have resolved my problem. Thanks for your help. You are so kind!

Li Zhenhai
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
China
Tel: 86-10-62773779
E-mail: shibalagu.thu at gmail.com

2007-10-12

======= 2007-10-11 21:26:32 您在来信中写道：=======


>------------------------------
>
>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
>
>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).
>
>
>On Thu, 11 Oct 2007 16:59:43 +0800
>  "shibalagu" <shibalagu.thu at gmail.com> wrote:
>> Hi, all,
>> 
>> I did a simulation on a system which had more than one molecule in it. After 
>>the simulation, I want to check the bond/angle/dihedral energy of one 
>>molecule in the system.
>> 
>> So I set a energy_grp named DNA in the mdp file, and used the command 
>>g_energy to calculate the energy on the energy_grp DNA. But I found that if I 
>>set a energy_grp in the mdp file, I still can only calculate the LJ/Coul 
>>energy on the molecule, and the bond/angle energy on the whole system, 
>>without the bond or angle energy on the molecule separately. 
>> 
>> Does anyone can help me? Thanks a lot!
>> 
>> 
>> Li Zhenhai
>> Department of Engineering Mechanics
>> Tsinghua University
>> Beijing 100084
>> China
>> Tel: 86-10-62773779
>> E-mail: shibalagu.thu at gmail.com
>> 
>> 2007-10-11
>> 
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>
>-----------------------------------------------------
>XAvier Periole - PhD
>
>1- Institute of Molecular Assemblies
>      City University of New York - USA
>2- Molecular Dynamics-Group
>      University of Groningen - The Netherlands
>http://md.chem.rug.nl/~periole
>-----------------------------------------------------
>
>