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" <[EMAIL PROTECTED]> 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: [EMAIL PROTECTED]
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
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