On 8/23/19 2:27 AM, Lei Qian wrote:
Thank you Dr. Lemkul, I continued to use the GROMOS 43a1p for my simulation. I did simulation for 2 proteins separately: one is WT, the other one is its one-residue mutant. And I finished em, NVT, NPT and 1 ns Production (4 steps) for both proteins. However, I found for each of these 4 above steps, the wall time was a lot more longer for mutant than WT protein. Actually I used the same set of parameters for both proteins: e.g. same mdp files for both protein in each step. Both proteins get acceptable results after 100-step NVT, 100-step NPT etc., but the wall-time for mutant was much more longer than WT. Could I ask the reason for this? Sorry for this inconvenience. Thank you for your time and all your help!
There is no way to know what is going on without seeing the .log files from the runs and knowing the commands you gave. If you want to share files, upload them to a file-sharing server and provide a link. The mailing list does not accept attachments.
-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.
