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

[Dawid das]

What do you mean by this question? Do you suggest to try reoptimization
starting from previous coordinates?


2014-08-11 12:36 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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.
>
> -Justin
>
>
>
>> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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