On 10/29/15 4:50 PM, Mishelle Oña wrote:
Hi!I am simulating a polimer of Polylactic acid with 30 monomers in a water system. For equilibrate the system I have made NVT, NPT and Process dynamics. The fiinal dynamic should have 40 000 frames but when I load it in VMD it has only 12 186 frames. Also the confout.gro file that result from the dynamic
VMD probably ran out of memory. What it thinks is there doesn't necessarily reflect reality. Use gmxcheck on the trajectory to verify its contents. Then try stripping out waters with trjconv and loading that in VMD.
-Justin
shows the polimer out of the box. I tried to center the polimer. At the end of the simultation this message appeared: Reading file topol.tpr, VERSION 4.5.5 (single precision) Starting 32 threads Making 3D domain decomposition 8 x 2 x 2 WARNING: This run will generate roughly 8233 Mb of data starting mdrun 'UNITED ATOM STRUCTURE FOR MOLECULE 3M9 in water' 10000000 steps, 20000.0 ps. NOTE: Turning on dynamic load balancing Writing final coordinates. Average load imbalance: 7.6 % Part of the total run time spent waiting due to load imbalance: 1.7 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 5 % Y 9 % Z 14 % Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 9229.145 9229.145 100.0 2h33:49 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 1786.838 66.381 187.233 0.128 gcq#247: "Let's Unzip And Let's Unfold" (Red Hot Chili Peppers) I don´t know if there is any error in the dynamic Then I opened the md.log file and in some steps there was this line:DD load balancing is limited by minimum cell size in dimension X YDD step 9998749 vol min/aver 0.625! load imb.: force 6.3% Please could anyone help me with an idea of what is happening? The previous simulation (NPT) doesn´t have this messages. Thanks a lot Mishelle
-- ================================================== 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.
