[gmx-users] problems in numbers of scale down by 0.95 in KALP in DPPC tutorial

[Justin Lemkul]

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

-- 
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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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