[gmx-users] problems in numbers of scale down by 0.95 in KALP in DPPC tutorial
jalemkul at vt.edu
Mon Aug 18 18:45:19 CEST 2014
On 8/18/14, 10:06 AM, Mahboobe Sadr wrote:
> Dear all,
> I am new in gromacs and specially in MD simulation of membrane protein, in part "define box and solvent" of justin's tutorial , in scaling down the lipids, I reached an area per lipid of ~69 A^2, after 4 times instead of 26 times....
> I don't know ,where I made a mistake?
Without seeing your exact commands and the corresponding output, there's nothing
to say. If you scale each time by 0.95, it is mathematically impossible to
arrive at a proper APL in this system with only 4 iterations. At least one of
your commands or preparation steps was wrong; the outcome is extremely reproducible.
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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