[gmx-users] A question about "blowing up"

Justin Lemkul jalemkul at vt.edu
Sat Mar 1 20:03:04 CET 2014

On 3/1/14, 8:26 AM, sujithkakkat . wrote:
> Hello Justin,
>    Thank you for the comments. While following the free energy calculation
> in the tutorial, I found that the constrains are switched on , while going
> from the minimization procedure to the NVT equilibration and the final
> results were pretty accurate. I guess that depends on the type of
> calculation and the system studied.

Yes, it does.  The geometry of a simple system like a single methane molecule in 
water (wherein the waters are pre-equilibrated) will not vary much during EM, so 
this is safe.  Be careful trying to pick and choose input files from various 
tutorials, it's not wise to assume that settings under one condition and with 
one goal in mind will work for other systems (not to mention force field issues).

> On a side note, I found the value of free energy calculated to be -9.56
> kJ/mol instead of -9.25 kJ/mol which you obtained. I am sure I followed
> everything as in the tutorial and I am using Gromacs-4.6.5. I hope the
> difference is not too worrying.

Not really, no.



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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