Jinyao Wang wrote:
From: XAvier Periole <x.peri...@rug.nl> Subject: Re: [gmx-users] how to
calculate the non-bond interaction between solvent and solvent in pure
solvent system To: Discussion list for GROMACS users
<gmx-users@gromacs.org> Message-ID:
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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)
This option can only calculate energies between non-overlapping groups.
That what he message is telling you: one atom can not be part of more than
one group.
If you actually have a simulation of pure solvent the total non-bonded
energy of your system seems to be what you are looking for!
Hello XAvier. Thank you for your reply. Because I don't know how to set the
option "energygrps" in rerun.mdp file, Now I still have no ideal for how to
calculate the intermolecular interaction energy in pure solvent system.
This has already been explained in several posts, you are just asking the same
thing over and over. The energy contributions you are looking for are
calculated by default in MD, there is no need for special energygrps, and you do
not have to re-run your simulation. Analyze the original energy file with
g_energy, as I have said several times. Have you done this? You will clearly
see the energy terms you want.
-Justin
Could you give me some details. Thanks in advance for your suggestion.
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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