[gmx-users] problem in NPT equilibration

[Justin Lemkul]

On 11/6/14 8:46 AM, soumadwip ghosh wrote:
> Dear Justin,
>                      Thank you so much for your suggestion. I did the NPT
> equilibration with nxtout=500 and got 1.05 bar pressure along with the
> density of the system = 1009 Kg/m3, which is in agreement to the SPC/E
> water model. In addition, I got the cell volume fixed at 285 nm3, which is
> expected. Now my question is, with the NVT (for 10 ns) step underway,
> should I look for point 1 and 2 or do I need to bother about something else
> in addition?
>
>                                                         1. cell volume to be
> fixed at 285 nm3 and
>                                                         2. temperature to be
> fixed at 300 K .
>
>
> I am slightly confused about the observations to be made in order to ensure
> proper equilibration after NVT. Please help.
>

In NVT, by definition the volume will not change; there is no scaling of the box 
vectors.  So observing a constant volume proves nothing.  With respect to 
temperature, it's not "fixed," as in "always the same value," rather it is 
probably better described as "conserved," or on average, equal to 300 K. 
Temperature converges very quickly, usually within a matter of tens (or at most, 
hundreds) of ps, depending on the thermostat being used.

-Justin

-- 
==================================================

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

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