[gmx-users] (Implicit solvation)Initial temperature changes to 0 K

[Justin Lemkul]

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
> appreciated
>

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 
zero.

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

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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