[gmx-users] Multiple runs for same system

Dr. Seema Mishra seema_uoh at yahoo.com
Mon Feb 26 00:07:40 CET 2018

Thanks Justin. Meaning I will simply set gen_seed as -1 instead of 173529. Right?
After this, how many runs will be performed? One? Then after the production run is finished, start it again with gen_seed=-1 for the second run?

This is to be done for 3 independent runs for same protein-ligand system.


    On Monday, 26 February 2018 4:16 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

Multiple runs are typically initiated simply by changing gen_seed when 
generating velocities at the outset of equilibration.

As for clustering, you'll have to explain what you mean. Clustering 
ligand poses? Protein? What? Does a Google search for "GROMACS 
clustering" or the help information for gmx cluster point you to 
anything useful


On 2/25/18 4:11 PM, Dr. Seema Mishra wrote:
> Or just direct me to the steps written anywhere....
>      On Saturday, 24 February 2018 3:51 PM, Dr. Seema Mishra <seema_uoh at yahoo.com> wrote:
>  Hi, Can anyone tell me the steps and commands for performing multiple runs of 50 ns for same protein-ligand system? Also the clustering for further analyses. Thanks.


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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