[gmx-users] Water molecule near protein surface cannot be settled.

Justin Lemkul jalemkul at vt.edu
Mon Aug 11 13:36:43 CEST 2014

On 8/11/14, 5:40 AM, Dawid das wrote:
> I forgot to mention that I get similar error for steepest descent
> minimization, not only conjugate gradient. Shall I change some options in
> *mdp files?

Does minimization proceed, i.e. the SETTLE problem is resolved?  It's not 
uncommon to see such messages in the very early stages of EM.  If they resolve 
and the energy and force values are sensible, there's no real problem.


> 2014-08-11 10:32 GMT+01:00 Dawid das <addiw7 at googlemail.com>:
>> Dear Gromacs experts,
>> I have encountered quite annoying problem again. When I try either
>> minimization or NVT dynamics of my solvated protein system I get message
>> like this:
>> step -1: Water molecule starting at atom 16281 can not be settled.
>> It is for couple of water molecules. I have checked visually where these
>> molecules are and for minimization they are near surface of protein (not
>> buried inside). I attach the link for *gro, *top, *log and other files.
>> What can I do about it?
>> http://www.speedyshare.com/rN4gx/mCherry7-min.tar.bz2
>> http://www.speedyshare.com/BnwU5/mCherry7-nvt-md.tar.bz2
>> http://www.speedyshare.com/3k9jz/charmm27-files.tar.bz2
>> Best wishes,
>> Dawid Grabarek


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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