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.
-Justin
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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.
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jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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