dear justin Thank you sincerely. I wish you the best. Regards mahboobeh
On Monday, April 28, 2014 2:48 PM, Justin Lemkul <jalem...@vt.edu> wrote: Please keep the discussion on the list. I can see from the other posts that providing this information to everyone likely would have been helpful. On 4/28/14, 2:44 AM, Mahboobeh Eslami wrote: > dear justin > I sent you the actual results for the repeated three times NPT stage: > > Energy Average Err.Est. RMSD Tot-Drift > ------------------------------------------------------------------------------- > Pressure -1.86895 1.7 74.4741 8.46672 (bar) > > Energy Average Err.Est. RMSD Tot-Drift > ------------------------------------------------------------------------------- > Pressure -1.01376 3.1 76.8484 0.464786 (bar) > > Energy Average Err.Est. RMSD Tot-Drift > ------------------------------------------------------------------------------- > Pressure 0.251751 3.7 80.9027 -1.89681 (bar) > > if i change tau_p for the second NPT stage to 6 i will get following result: > > Energy Average Err.Est. RMSD Tot-Drift > ------------------------------------------------------------------------------- > Pressure 1.20898 1.9 78.1862 0.931217 (bar) > > Energy Average Err.Est. RMSD Tot-Drift > ------------------------------------------------------------------------------- > Pressure -0.514578 1.8 78.6336 -2.57617 (bar) > > Energy Average Err.Est. RMSD Tot-Drift > ------------------------------------------------------------------------------- > Pressure 5.67055 1.9 80.5453 2.32409 (bar) > Increasing tau_p relaxes the stringency of the barostat; I would expect the results to be "worse" when doing so. The bigger point here is that none of this looks anomalous to me. You're doing short NPT (100 ps), during which the pressure is unlikely to relax fully. More importantly, look at the actual numbers: -2 ± 75, -1 ± 77, 0.2 ± 81. Are any of these significantly different from the target value of 1 or do they differ significantly from one another? I'd say no. Pressure is ill-defined and subject to very large fluctuations. I wouldn't call any of this cause for concern. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
