Hello All -- I'm trying to do a normal modes analysis of a fairly large crystal system (~20,000 atoms) in double-precision GROMACS. The system is xy periodic with 2 9-3 walls, and has periodic molecules. I first minimized the structure with L-BFGS to 1e-5 tolerance with switched vdW interactions and PME electrostatics (3dc geometry).
When I tried to run g_nmeig on the matrix, I received the following error message from the shell /var/spool/pbs/mom_priv/jobs/2480011.lionxj.rcc.psu.edu.SC: line 7: 3205 Segmentation fault g_nmeig_d -f wall3_nm -s wall3_nm -T 300 -first 1 -last 20000 -of wall3_efreq -ol wall3_eigval -v wall3_eigvec >&nm.g_nmeig The last thing written to the g_nmeig output is Reading file wall3_nm.tpr, VERSION 4.5.5 (double precision) Reading file wall3_nm.tpr, VERSION 4.5.5 (double precision) Reading double precision matrix generated by Gromacs VERSION 4.5.5 I was able to successfully run NMA using the same code on a similar system that was only 1/3 of the current size (reaction-field-zero electrostatics) and also on a system 1/3 of the size with xyz periodicity and PME electrostatics, and received no segmentation fault error. I'm a little bit baffled about the source of the segmentation error, because I would have expected it to crash during the Hessian calculation if there were a problem with allocating system memory or essentially singular forces. Has anyone else encountered a similar problem? Thanks in advance for your help. -- Mike Howard -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
