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!
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.
Jinyao Wang
wan...@ciac.jl.cn
2009-10-10
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