Dear users I used gromacs for my system include CNT-water-ion-protein (400,000atom), I used grompp without error.
after used mdrun with 16 node on cluster, I get this error: Reading file nvt.tpr, VERSION 4.0.7 (single precision) Loaded with Money NOTE: Periodic molecules: can not easily determine the required minimum bonded cut-off, using half the non-bonded cut-off Will use 15 particle-particle and 1 PME only nodes This is a guess, check the performance at the end of the log file ------------------------------------------------------- Program mdrun, VERSION 4.0.7 Source code file: domdec.c, line: 5888 Fatal error: There is no domain decomposition for 15 nodes that is compatible with the given box and a minimum cell size of 3.75 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition ------------------------------------------------------- "Good Music Saves your Soul" (Lemmy) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 16 --------------------------------------- my box size is 14*14*18. I used mdrun -rdd 1 , gromacs run without error is it correct or not? I get this error in NVT (Em run without error. Best Regards. Hamid Mosaddeghi -- View this message in context: http://gromacs.5086.n6.nabble.com/error-in-gromacs-4-0-7-Source-code-file-domdec-c-line-5888-tp5006245.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
