Most likely you do something wrong in energy minimization step: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.htmlMake sure you produce plot similar like in that page with your system before proceeding further with minimized system.
On Wednesday, October 4, 2017, 9:18:48 PM GMT+3, Albert <mailmd2...@gmail.com> wrote: Hello, I am using the following .mdp file for protein BG solvent simulations. However, the job always failed with the following messages: vol -0.00! imb F 22% step 144100, remaining wall clock time: 207 s vol -0.00! imb F 23% step 144200, remaining wall clock time: 207 s vol -0.00! imb F 23% step 144300, remaining wall clock time: 207 s vol -0.00! imb F 23% step 144400, remaining wall clock time: 207 s ------------------------------------------------------- Program gmx mdrun, VERSION 5.1.4 Source code file: /icm/home/albert/tmp/gromacs-5.1.4/src/gromacs/mdlib/nsgrid.c, line: 633 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 ind has value 131. It should have been within [ 0 .. 131 ] The initial system seems to be all right since it is a liner peptide. The initial energy of the peptide is also very low. I am not so sure whether my .mdp is correct or not.... Thank you very much. define = -DREST_ON -DSTEP_NVT integrator = md dt = 0.001 nsteps = 300000 nstlog = 1000 implicit_solvent = GBSA gb_algorithm = OBC ;nstgbradii = 1.0 rgbradii = 1.0 gb_epsilon_solvent = 80 gb_dielectric_offset = 0.009 sa_algorithm = ace-approximation sa_surface_tension = 0.0054 pbc = no coulombtype = cut-off cutoff-scheme = group nstlist = 20 rlist = 1.0 tcoupl = Nose-Hoover tc_grps = Protein tau_t = 1.0 ref_t = 310 ; constraints = h-bonds constraint_algorithm = LINCS ; nstcomm = 100 comm_mode = angular comm_grps = Protein ; gen-vel = yes gen-temp = 310 gen-seed = -1 ; refcoord_scaling = com -- 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. -- 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.