[gmx-users] (no subject)

[Hassan Aaryapour]

Dear Justin,
Where can I find the primary literature for setting up proper parameters in
mdp files? I downloaded all literatures in "General Information" section in
link below (http://ffamber.cnsm.csulb.edu/ffamber.php), but I did not find
anything related to the Cutoffs.

Regards
Hassan


On Sun, Jun 28, 2015 at 10:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/28/15 3:22 PM, Vidyalakshmi CM wrote:
>
>> Hi,
>>
>> You may use the mdp files from the tutorial
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
>> (It has topologies for energy minimzation, nvt and npt simulations and md
>> simulations run).
>>
>>
> The tutorial .mdp settings are for OPLS-AA and may not be generally
> applicable to any other force field.  This is a non-trivial consideration
> in running simulations properly.
>
> "AMBER force field" is a bit generic; different parameter sets use subtly
> different parameters.  The primary literature for the parameter set of
> interest will contain the proper run settings.  Use whatever those settings
> are.
>
> -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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