[gmx-users] Protein-ligand complex simulation and ATBserver file

Justin Lemkul jalemkul at vt.edu
Thu Dec 20 19:53:44 CET 2018

On Thu, Dec 20, 2018 at 10:05 AM Prasanth G, Research Scholar <
prasanthghanta at sssihl.edu.in> wrote:

> Dear Sir,
> Thanks a lot for the inputs. I tried incorporating the forcefield
> parameters (directory) obtained from the atbserver in the working
> directory. When i was trying to convert the protein.pdb to .gro, I noticed
> that the forcefield showed up in the menu as one included in local
> directory, just as it does for cgenff in the tutorial.
> I chose it to prepare the protein.gro file and then incorporated the
> jz4.itp into the topology file of protein.
> I was able to overcome the issues and complete npt and nvt equilibration.
> Will proceed with the mdrun tomorrow morning.
> Can you please suggest a solution for resuming the mdrun, in case there is
> an interruption in the connectivity with the server. As i am running the
> simulation from a laptop, I might not be able to leave it on through out.


Checkpointing makes continuing a simulation seamless.




Justin A. Lemkul, Ph.D.

Assistant Professor

Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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


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