[gmx-users] tip5p and charmm
jalemkul at vt.edu
Tue Mar 4 02:05:18 CET 2014
On 3/3/14, 7:07 PM, Rafael I. Silverman y de la Vega wrote:
> Hi all,
> I saw a post from a little while ago where someone (Justin?) said that
> tip5p wasnt recommended for use with charmm27, so tip5p wanst included in
> the watermodels.dat file.
> I have found that my system blows up with tip5p, but tip4p and tip3p energy
> minimize just fine.
> And, I am also having problems getting pymol and chimera to open the .gro
> file produced by mdrun with tip4p and tip5p. (VMD opens the .gro file
> My questions are, is tip5p/charmm27 a good combination to use when trying
> to model protein-prosthetic.group-water interactions?
Doubtful. Clearly your findings indicate the combination is not stable, and
that is my recollection from previous posts on the list, as well. We develop
CHARMM in the context of TIP3P. If something else happens fortuitously to work,
great, but that's coincidence. People have used other water models and have
reported some levels of success (stable simulations, at least), but it's not
what we recommend because it's not consistent with the parametrization.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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