On 6/1/15 6:39 AM, Kevin C Chan wrote:
Dear Users, I have encountered "Fatal error: The X-size of the box times triclinic skew factor is smaller than the number of DD cells times the smallest allowed cell size" during a pre-equilibrium (NPT) run. It is NOT an annealing process and temperature was coupled to 300K, pressure to 1.0 bar. It was a 1000-water plus 100 amino acid system. I have gone through the mailing archive and it was reported that this might result from too-fast-shrinking systems. However I intended to shrink the box during the NPT run as initially it was generated using genbox tool and what I wanted to fix is only the number of solvent and additional particles. As I do not know the suitable box size for the system so I guess a little bigger box size (6 nm) and let it shrink during the NPT run. This was successful with a previous system (1000 water, 50 amino acids) and the box size shrank to 4.X nm. Would this be a wrong approach? And how could I deal with the reported error?
The error suggests indeed the box is collapsing, so your initial box is too large. The box vectors are written to the .edr file so you can see this for yourself if enough frames are written before the crash. Either (1) calculate a proper size for the box, even if it is based on a rough estimate of the density this is trivial to do and/or (2) relax the barostat coupling time to allow for a more gentle equilibration.
-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.
