On Thu, Dec 20, 2018 at 10:05 AM Prasanth G, Research Scholar < prasanthgha...@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. > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts Checkpointing makes continuing a simulation seamless. -Justin -- ========================================== 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 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ========================================== -- 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.
