[gmx-users] pressure and temperature coupling is off in vacuum simulations
jalemkul at vt.edu
Wed Sep 23 13:35:23 CEST 2015
On 9/23/15 6:37 AM, Erik Marklund wrote:
> On 23 Sep 2015, at 08:28, Mark Abraham
> <mark.j.abraham at gmail.com<mailto:mark.j.abraham at gmail.com>> wrote:
> On Wed, Sep 23, 2015 at 8:32 AM tasneem kausar
> <tasneemkausar12 at gmail.com<mailto:tasneemkausar12 at gmail.com>> wrote:
> Dear Gromacs users
> I have performed MD simulation for protein in vacuum condition.
> That's super artificial, so nothing else you do matters :-)
> This tongue-in-cheek reply does deserve a comment. Indeed the vacuum
> conditions introduce additional accuracy problems to the physical model, and
> one must be aware of this as to not over-interpret the results. A very fair
> point. That is not to say that we cannot learn from vacuum simulations of
> macromolecules however. Surely, the approach to, for instance, treat the
> protein as perfect ball also suffers from accuracy problems?! Or do you
> object to the notion of gas-phase proteins are artificial? Sure, it rarely
> happens in cellular processes (to my knowledge), but mass spectrometry is an
> extremely useful technique for the biosciences and requires gas-phase
> samples. As such experiments become more advanced (and they do, rapidly),
> there are more and more reasons to model the experiments. We do not know the
> objective here, and should not be so quick to dismiss the investigation.
Erik, perhaps you can comment on an issue I've wondered about: to what extent do
any of the force fields available in GROMACS prove useful in the gas phase?
They are all designed for condensed phase systems, and are parametrized to
reproduce behavior in/interactions with water. The intrinsically overestimated
dipoles (required for the additive approximation) would yield interactions in
vacuo that are generally much too strong, or incorrect altogether. I'd be
curious to get your opinion on this.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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