jalemkul at vt.edu
Sat May 14 11:37:31 CEST 2016
On 5/14/16 2:25 AM, Ms. Nikita Bora wrote:
> 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
Longer cutoffs = more interactions to compute.
Cutoffs are part of the force field. Don't change them from prescribed values
without very strong justification.
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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
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