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 <[email protected]> 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 > 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 > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University
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