Dear all, I am trying to simulate a graphene sheet, periodic in xy. I am using Gromacs 4.5.5. My simulation fails before I can complete an energy minimisation in mdrun.
For the force field I added the following lines to atomname2type.n2t of a copy of oplsaa.ff 3 C opls_145 0.0 12.011 3 C 0.140 C 0.140 C 0.140 4 C opls_145 0.0 12.011 2 C 0.140 C 0.140 For the structure preparation I used Atomic Simulation Environment python library ase.structure to create a sheet that is 17.04 nm by 9.38048587 nm (this is the exact precision provided by ase). After this I used g_xtop to create the topology. g_x2top -f graphene.gro -o cnt.top -name GRA -pbc I also used editconf to center the graphene sheet in a box that is 17.04 nm by 9.38048587 nm by 20 nm. The mdp file for the energy minimisation is as follows integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) periodic_molecules = yes I was able to run x2top and grompp successfully. With mdrun, I receive the error Warning: 1-4 interaction between 5761 and 5918 at distance 16.685 which is larger than the 1-4 table size 2.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, .... I have checked both atoms 5761 and 5918 and they lie right on the edge of the box (the graphene sheet is orientated in the xz axis): C 5761 0.799 10.000 0.071 C 5918 0.922 10.000 16.898 It seems like there is a problem with the periodicity. Have I defined a box that is too small? I appreciate any assistance. -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
