On 9/17/13 8:47 AM, shahab shariati wrote:
Dear Justin
Very very thanks for your quick reply.
I am very confused and amazed.
After visualization of atom 618 ( where the maximum force is),
what should I do to resolve me problem.
Any help will highly appreciated.
I honestly have no idea. There's something nasty going on there, but only you
have the ability to see it. You can always try a smaller value of emstep, a
different EM algorithm, etc. Try setting nstxout = 1 and visualize the entire
EM "trajectory" to see where things start to go out of control. And finally, if
it really isn't working, ask the people who provided the coordinates - they're
supposed to be pre-equilibrated, so if you can't get it to minimize, maybe
there's something wrong that's happened before you even got your hands on the file.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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