Jinyao Wang wrote:
Jinyao Wang wrote:
Hi gmx-users锛?
I want to calculate the non-bond interaction (LJ+Coulomb) between solvent
and solvent in pure solvent system. After the simulation of my pure
solvent system, I calculated the interaction between solvent and solvent
using the rerun option of the "mdrun program". First, I set the
energygrps = sol sol in rerun.mdp file. Then, I make the grompp program
like this, grompp -f rerun.mdp -c conf.gro -n index.ndx -p pure.top -o
rerun.tpr But this step has a fatal error: Atom 1 in multiple energy Mon.
groups (1 and 2)
I don't know how to solve the problem and I want to know whether this
method is effective for calculating the interaction between solvent and
solvent in pure solvent system.
Any suggestion will be appreciated.
These terms should already be present in the .edr file. Run g_energy and
have a look.
-Justin
Hi Justin, Thank you for your reply. But I still don't know how to set the
"energygrps" option in the rerun.mdp for calculating the interaction between
solvent molecule and solvent molecule in pure solvent system. As you said
that these terms should be obtained running the g_energy,could you give me
some details about the "energygrps" option in rerun.mdp file or how to
calculate the intermolecular interaction in pure solvent system. Thanks in
advance.
If you have a pure solvent system, there is no way to set separate energygrps,
as you found out earlier. There is also no need to re-run your simulation. Use
g_energy to analyze your original ener.edr file; you will see the LJ and
Coulombic terms in the list of options.
-Justin
Jinyao Wang wan...@ciac.jl.cn 2009-10-12
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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