[gmx-users] Protein-DNA simulation LINKS error

[Justin Lemkul]

On 6/23/15 7:13 AM, Timofey Tyugashev wrote:
> I'm trying a few simulations of a enzyme-DNA complex and while in short
> timeframes (up to 5ns) the behaviour looks quite normal, a 10ns simulation
> crashes with numerous LINCS warnings.
> Maybe there are some errors in mdp configuration file? To mine inexperienced eye
> they look good enough.
> I'm using AMBER99SB-ILDN with TIP3 water model and 1.0 dodecahedron water box,
> system requires around 30 Na atoms to compensate the charge. I also create a
> combined group Protein_DNA using make ndx.
> Here are the MDPs:
>
> Ions: http://pastebin.com/xCUqiDM0
> EM: http://pastebin.com/WcXdXBWf
> NVT: http://pastebin.com/sdVqfGDM
> NPT: http://pastebin.com/AsMVC7yH
> MD: http://pastebin.com/sne7Fpzt
>
> Any help?

AMBER99sb-ILDN uses different cutoffs so correct those, but that alone is not 
necessarily to blame for the crash.  In general, here's the usual 
troubleshooting protocol:

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

-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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