[gmx-users] simulation_time

Justin Lemkul 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.


> ___________________
> D I S C L A I M E R
> This e-mail may contain privileged information and is intended solely for
> the individual named. If you are not the named addressee you should not
> disseminate, distribute or copy this e-mail. Please notify the sender
> immediately by e-mail if you have received this e-mail in error and
> destroy it from your system. Though considerable effort has been made to
> deliver error free e-mail messages but it can not be guaranteed to be secure
> or error-free as information could be intercepted, corrupted, lost, destroyed,
> delayed, or may contain viruses. The recipient must verify the integrity of
> this e-mail message.


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


More information about the gromacs.org_gmx-users mailing list