On 2/25/18 6:07 PM, Dr. Seema Mishra wrote:
Thanks Justin. Meaning I will simply set gen_seed as -1 instead of 173529.
Right?
However you want to do it, either by specifying a seed or letting grompp
generate one. Some prefer the former for reproducibility, but given all
the things that can affect binary reproducibility, I don't think it's a
big concern.
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?
Each .tpr specifies one initial set of conditions for a simulation. If
you want another simulation, generate another .tpr that specifies a
different set of conditions.
-Justin
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 <jalem...@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_...@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
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
