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

[Justin Lemkul]

On 8/11/14, 8:17 AM, Dawid das wrote:
> What do you mean by this question? Do you suggest to try reoptimization
> starting from previous coordinates?
>

You posted a SETTLE warning from step -1 during EM, but did not indicate if the 
EM proceeded and finished.  That's what I'm asking.  What happened next?  Did EM 
finish?  Did it yield a sensible energy and maximum force?

-Justin

>
> 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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-- 
==================================================

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

==================================================