Hey :) A little while ago I tried growing in molecules in a solution starting from shrunken coordinates. It would have been very useful if the box also had taken part in the energy minimization... That would have saved quite bit of trouble relaxing with NPT MD.
Just my two cents :) Tsjerk On Dec 29, 2010 7:32 PM, "Justin A. Lemkul" <jalem...@vt.edu> wrote: MyLinkka wrote: > > Hi Justin, > > Thanks for your answer! > > As far as I understood, the virial ... I suppose, in theory, it's possible to use an EM algorithm to optimize a box. But for most systems, like a box filled with solvent, during EM the positions move very little and I'd be willing to bet the box wouldn't even change. I guess it depends on what you're looking to do, but for a system that hasn't even been equilibrated under the desired thermodynamic conditions (with a proper velocity distribution applied to the atoms), I don't see any real value in trying to obtain what you might consider an "optimized" box for a system that is not at equilibrium. The box stabilizes during NPT equilibration. -Justin > Ting Li > > > On 12/25/2010 3:41 PM, Justin A. Lemkul wrote: >> >> >> >> MyLinkka wrote: >>> >>>... ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MI... gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users ...
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