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

Xavier Periole X.Periole at rug.nl
Thu Oct 11 14:25:35 CEST 2007

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).

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

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