[gmx-users] Potential Energy

[Justin A. Lemkul]

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

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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