[gmx-users] how to calculate the non-bond interaction between solvent and solvent in pure solvent system

[Justin A. Lemkul]

Jinyao Wang wrote:
> Hi gmx-users，
> 
> 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

> 
> 
> 
> 　　　　　　　　Jinyao Wang 　　　　　　　　wangjy at ciac.jl.cn 　　　　　　　　　　2009-10-10
> 
> 
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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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