[gmx-users] TIP5P - water molecules cannot be settled

[Justin Lemkul]

On 3/3/16 5:27 PM, Irem Altan wrote:
>
>
> On 3/3/16 5:16 PM, Irem Altan wrote:
> Hi,
>
> Thanks for your reply. I have checked step12b.pdb and step12c.pdb, and I didn’t observe a deformation in the shape of the molecule in question. It doesn’t look like there is any overlap or clash either. I have also tried to comment out the #ifndef FLEXIBLE block and only leave the settles block uncommented. It results in the same error. How can I check if it is the combination of water models and protein force fields that cause the problem?
>
>
> Do people use AMBER + TIP5P often?  Does it run with AMBER + TIP3P?
>
> I have no knowledge of AMBER + TIP5P, but I have used AMBER + TIP3P, TIP4P, SPC, and SPC/E without problems.
>
> Also realize that water not being settled doesn't necessarily mean you need to troubleshoot the water, it's just that it's the first thing that fails when something goes haywire.
>
> What would you recommend me to do in order to troubleshoot the problem?
>

Answer the question I posed before: "Does it run with AMBER + TIP3P?"

If it does, likely the use of TIP5P is inappropriate.  If it crashes, then you 
have a fundamental problem with your protein or some aspect of your simulation 
settings.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

If I had a nickel for every time I posted that link... ;)

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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