[gmx-users] Different Results with Different Platforms

[Justin Lemkul]

On 10/5/16 8:45 PM, Kelechi Okoroafor wrote:
> Thank you very much, James.
> My apologies, I miscommunicated myself.
>
> I meant to say that I used NPT simulation to equilibrate the pressure
> to 1bar as desired. I had planned to do NVT simulation after the NPT
> simulation, expecting the pressure to fluctuate reasonably about the
> mean value of 1bar.
>
> Unfortunately, editconf edited the trajectory such that during the NVT
> simulation, the pressure fluctuated about the mean value of 900bar
> causing the observed unusual behaviour.
>

I don't see how that's possible.  If you move from NPT -> NVT, the ensemble that 
is preserved is the one that is present in the final snapshot; even if the 
average over the NPT run is 1 bar, there is no guarantee that instantaneous 
value is 1 bar, though the density is likely correct.

Where was editconf involved in this process?  If you're continuing a run and 
changing ensemble, you should be invoking grompp -t with the previous 
checkpoint.  Any other use of GROMACS tools introduces discontinuity.

-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 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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