[gmx-users] Re:Re: how to calculate the non-bond interaction between solvent and solvent in pure solvent system (Justin A. Lemkul)

[Justin A. Lemkul]

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 　　　　　　　　wangjy at 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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