[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 jalemkul at vt.edu
Mon Oct 12 04:47:15 CEST 2009

Jinyao Wang wrote:
>>> 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
> Hi Justin, My simulation system is pure benzaldehyde system. I set the option
> nrexcl = 3. So I think the LJ and Coulombic terms include intermolecular
> interaction energy and intremolecular interaction eneryg (e.g. between atom
> and atom)

This is important information!  Your original message had SOL as the groups you
were trying to define, so I assumed you were working with water.  Since you have 
a homogeneous system, you cannot use energygrps.  What would probably be a 
better approach would be to construct a new topology in which [exclusions] are 
defined among all the atoms.  Then re-run with the new topology.


>         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


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