Dear Justin, Thank you very much, that works.
Regards, Beng Hau ________________________________________ Date: Thu, 29 Aug 2013 08:01:10 -0400 From: Justin Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] Creating an infinite sheet of graphene To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <521f3806.6080...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 8/29/13 5:28 AM, #TAN BENG HAU IAN# wrote: > 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. > Yes, the box is too small. If it fits the coordinates exactly, there is no room for the bonds that occur across periodic boundaries. You need to leave a distance around the whole structure of 1/2 a C-C bond length so that the bonds can be properly constructed. Otherwise, you just have two carbon atoms directly on top of one another at each boundary. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- 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
