[gmx-users] Re: grompp for minimization: note & warning

Justin Lemkul jalemkul at vt.edu
Tue Sep 17 14:51:45 CEST 2013

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 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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