[gmx-users] simulation_time

[Justin Lemkul]

On 5/16/16 12:23 AM, Ms. Nikita Bora wrote:
> ---------------------------- Original Message ----------------------------
> Subject: Re: simulation_time
> From:    "Ms. Nikita Bora" <niki24 at tezu.ernet.in>
> Date:    Mon, May 16, 2016 9:42 am
> To:      niki24 at tezu.ernet.in
> --------------------------------------------------------------------------
>
> Respected Sir,
>
> Thanks for the reply. I would further like to know that according to this
> tutorial
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html)
> the rvdw=rcoulomb=1 is used for the protein while according to this
> tutorial
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html)
> rvdw=rcoulomb=1.4 is used. why a different value for the simple protein
> and protein-ligand complex is used??
>

Different force fields, different settings.

-Justin

>
>> Respected Sir,
>>
>> Recently i followed your tutorial for simulation of a 50 ns final mdrun
> of protein-ligand complex where the value of rvdw=rcoulomb=1.4 was used.
> The simulation runned at aorund 10 ns/day . While for the same  complex
> when rvdw=rcoulomb=1 is made the run was 10 ns/day.
>>
>> Sir i would like to know is there any standard value for rvdw,rcoulomb
> and why a longer time is taken for 1.4 value
>>
>>
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-- 
==================================================

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

==================================================