[gmx-users] Protein-DNA simulation LINKS error

[Erik Marklund]

The vsite parameters are not complete for DNA/RNA. Perhaps you have faster oscillations in your system than you intended to have.

Erik

> On 23 Jun 2015, at 21:15, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> 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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