[gmx-users] protein water contacts
jalemkul at vt.edu
Mon Mar 31 23:49:54 CEST 2014
On 3/31/14, 2:03 PM, pratibha wrote:
> Hi all
> I have done simulations of one molecule of protein using explicit solvent at
> two temperatures 300K and 400K. On calculating protein water contacts using
> g_mindist, I could see that these contacts are lower at higher temperature
> (even at 0ns simulation) of 400K compared to that at 300K, although we
> expect it to increase with temperature due to increase in exposed surface
> area on account of thermal unfolding.
> Is there something wrong in my simulations or in my reasoning?
If the increase in contacts is predicated upon unfolding, did you establish an
unfolded state in some meaningful way (radius of gyration or loss of native
structure, for instance)? Is your ensemble NVT or NPT? If the latter, I would
not think it obvious that you will necessarily have more water-protein contacts,
because the water density will decrease as a function of temperature (and at 400
K, the water is boiling). Also, are you measuring contacts between all atoms or
just heavy atoms? Measuring all-atom contacts gets muddled because all the H
contacts diminish the sensitivity of the measurement.
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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