[gmx-users] Multiple runs for same system

[Dr. Seema Mishra]

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.

Seema
 

    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

-Justin

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
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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