[gmx-users] (Implicit solvation)Initial temperature changes to 0 K
jalemkul at vt.edu
Wed Feb 19 14:40:53 CET 2014
On 2/19/14, 1:55 AM, nichith wrote:
> I am trying to run a simulation of single Na ion in implicit solvent(water),
> with OPLSAA FF in gromacs 4.5.7. After running the simulation and viewing
> the .log file I find that the initial temperature is set to 0 K even though
> I have mentioned a ref_t as 300 K. Why does this happen? Any help is much
Since you haven't specified comm-mode, it will default to Linear, which removes
translational motion. You have 3N-2 = 1 degree of freedom to start
(translation), and then you're removing that degree of freedom with COM motion
removal, so its velocity is continually reset to zero, hence the temperature is
There really isn't much point to this simulation; you have one point that cannot
vary over time! A single-point energy evaluation is all you need.
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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