Dear Gromacs-Users, Is there anybody have met such problem before? I did NTP simulation for POPE system downloaded from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies. It can run for even 10 ns with single precision GROMACS on many processors or with double precision GROMACS on 1 or 2 processors, but crash at about 100ps with double GROMACS on more than 2 processors. The same thing didn't happen for a NTV simulation. I don't think it can be ascribed to the initial structure, because I used the same initial structure and input files for tests. Which one do you prefer for MD simulation, single or double precision?
Here is the error message: Program mdrun_mpi_d, VERSION 3.3.2 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value 4421. It should have been within [ 0 .. 4212 ] ------------------------------------------------------- I compiled GROMACS on Linux x86_64 with mvapich-0.9.9, this is how I complied it: #!/bin/csh -f setenv CC icc setenv CXX icpc setenv F77 ifort setenv MPICC mpicc setenv CFLAGS "-O3 -fPIC -align -Zp8 -axW -unroll -Wno-deprecated -ip" setenv CXXFLAGS "-O3 -fPIC -align -Zp8 -axW -unroll -Wno-deprecated -ip" setenv FFLAGS "-O3 -fPIC -align -Zp8 -axW -unroll -Wno-deprecated -ip" setenv CPPFLAGS "-I/home/yz30/Intel/FFTW-3.1.2-Lib/include" setenv LDFLAGS "-L/home/yz30/Intel/FFTW-3.1.2-Lib/lib -L/usr/X11R6/lib64" ./configure --prefix=/scratch/yz30/Intel/Gromacs-3.3.2-FFTW3 --enable-double --with-fft=fftw3 \ --enable-mpi --program-suffix=_mpi_d --disable-nice Thanks in advance. _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
