On 10/5/16 8:45 PM, Kelechi Okoroafor wrote:
Thank you very much, James. My apologies, I miscommunicated myself. I meant to say that I used NPT simulation to equilibrate the pressure to 1bar as desired. I had planned to do NVT simulation after the NPT simulation, expecting the pressure to fluctuate reasonably about the mean value of 1bar. Unfortunately, editconf edited the trajectory such that during the NVT simulation, the pressure fluctuated about the mean value of 900bar causing the observed unusual behaviour.
I don't see how that's possible. If you move from NPT -> NVT, the ensemble that is preserved is the one that is present in the final snapshot; even if the average over the NPT run is 1 bar, there is no guarantee that instantaneous value is 1 bar, though the density is likely correct.
Where was editconf involved in this process? If you're continuing a run and changing ensemble, you should be invoking grompp -t with the previous checkpoint. Any other use of GROMACS tools introduces discontinuity.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
