[gmx-users] Potential Energy

Yanmei Song ysong30 at asu.edu
Wed Jan 27 00:57:09 CET 2010

Dear Justin:

I finally figure out that the problem comes from the Coulomb 1-4
interactions defined by [pairs] part. When I remove this parts, the energy
minimization ends with a big negative number. Thanks for your help.

On Tue, Jan 26, 2010 at 4:24 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> Yanmei Song wrote:
>> Dear Justin:
>> Sorry, that itp is the original one generated by PRODRG. Also I have
>> modified it based on a optimized force field of the molecule. (See attached
>> file and the literature of the force field). But still the potential energy
>> is positively 1e2 and why the system can run well and I can get the
>> reasonable density? Except charge, can you see any obvious mistakes of the
>> itp file? since even if the parameter is not so optimized, I should not get
>> such a big positive potential energy.
> If you have 27800 molecules, that means you have almost 56000 -OH groups
> and even more potential H-bond acceptors with the ether oxygens.  If there
> are a lot of unoccupied hydrogen bonding groups, then you have a lot of
> electrostatic interactions that are unsatisfied.  The same situation can
> occur with, for example, a protein in vacuum.  I'm assuming this is the
> case, but you haven't said whether or not there's solvent.
> As for whether or not you can lump the hydrogen charges into the carbon
> atoms, that can be debated.  The parameter set you've used has no direct
> relevance to the Gromos parameter set from which you're (presumably) taking
> atom types.  But if you're able to produce a substantial amount of
> experimental observables, you may be able to justify your methods.
> -Justin
> --
> ========================================
> 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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Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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