[gmx-users] Protein-DNA simulation LINKS error

[Timofey Tyugashev]

I have ordinary DNA and an oxoguanine site? What actions should I take 
to correct these vsite parameters?
> Message: 1
> Date: Tue, 23 Jun 2015 22:24:20 +0000
> From: Erik Marklund <erik.marklund at chem.ox.ac.uk>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Protein-DNA simulation LINKS error
> Message-ID: <61EDBF38-6D1F-4089-8EBE-03CAAAFF6F14 at chem.ox.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> 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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