Hello, I'm getting problems to simulate amorphous silica with potentials I made myself : table_Si_Si.xvg, table_Si_O.xvg, table_O_O.xvg and table.xvg (which should not be used as all the possible non-bonded interactions are given in the three previous tables).
The generation of the topology file with grompp works well but when I'm try to simulate my system (mdrun), Im getting a segmentation fault. Am I missing something in the topology file or grompp.mdp file ? I just want to have the non-bonded interactions defined in my tables to be applied. My topology and input file are hereafter. I can give you my tables.xvg but they are too big to be posted on the forum. Thanks a lot My topology file TOPOL.TOP is the following : [ defaults ] 2 1 0 [ atomtypes ] ; name mass charge ptype c6 c12 O 15.99940 -0.955209 A 1.0 1.0 0.0000; Si 28.08550 1.910418 A 1.0 1.0 0.0000; [ nonbond_params ] O O 2 1 1 1 O Si 2 1 1 1 Si Si 2 1 1 1 [ moleculetype ] O 0 [ atoms ] 1 O 1 O O 1 -0.955209 15.99940 [ moleculetype ] Si 0; [ atoms ] 1 Si 1 Si Si 2 1.910418 28.08550 [ system ] Silica [ molecules ] O 384 Si 192 and my mdrun input file GROMPP.MDP is : title = 576-atoms a-SiO2 model 01 cpp = cpp define = integrator = md dt = 0.001 nsteps = 25000 ; Coulomb type coulombtype = User vdwtype = User rvdw = 1.0 rlist = 1.0 rcoulomb = 1.0 fourierspacing = 0.1 ewald_rtol = 1e-5 energygrps = Si O energygrp_table = Si Si Si O O O ; Temperature Coupling tcoupl = nose-hoover tc_grps = System tau_t = 0.02 ref_t = 7000 gen_vel = yes gen_temp = 7000 gen_seed = -1 ; Simulated Annealing ; annealing = single ; annealing_npoints = 3 ; annealing_time = 0 56 150 ; annealing_temp = 5000 5000 300 ; Output parameters nstxout = 100 nstxtcout = 1000 -- ----------------------------------------------------------- David Waroquiers, Phd Student European Theoretical Spectroscopy Facility (ETSF) Unité de Physico-Chimie et de Physique des Matériaux (PCPM) Université Catholique de Louvain (UCL) ----------------------------------------------------------- Address : Bâtiment Boltzmann Place Croix du Sud, 1 1348 Louvain-la-Neuve, Belgique ----------------------------------------------------------- E-mail : [email protected] Tel : + 32 (0)10 / 47 28 38 Fax : + 32 (0)10 / 47 34 52 ----------------------------------------------------------- _______________________________________________ gmx-users mailing list [email protected] http://lists.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
