Dear list members, I am trying to simulate an infinite layer of quartz in Gromacs. Due to my needs (afterwards I need to place a large molecule on top of it) the surface must be at least 12x12 nm^2. I generated the input files from a pdb file of the structure, and adapted the OPLS force field to my current needs, adding some compatible parameters from the literature. I am using the parameter
periodic-molecules = yes in the mdp file, because if not I have a warning about inconsistent shifts. As Gromacs could not minimize the structure, I just took a smaller version of the surface compatible with the cut-off radius, with the idea to minimize it and then simply replicate it to obtain the large surface I need. Now Gromacs was able to minimize the small system, but I realized that it was not taking into account the bonded potentials across boundary conditions. I did not manage to obtain a topology file by the use of pdb2gmx which included the bonded potentials across periodic boundary conditions, so I wrote my own program to generate them. I checked that the missing interactions were properly added. I run again the simulation with the right topology file for the small system, and everything worked. The problem is that, when I replicate the minimized structure in the x and z directions to obtain the structure I need (and generating a new topology file with the right bond information, changing the simulation box size properly, etc), Gromacs still can not minimize the system, so that it does not 'explode' when I later try to minimize the system after generating a velocity for every atom, even at very low temperatures. I also tried to minimize the original, large simulation box with a proper topology file, to change the minimization method, the minimization step, tried different constraints, etc, but without success. I have been working on this problem for three weeks now and I run out of ideas, can any of you help? I copy one example of mdp I used. ;constraints = all-bonds constraints = none ; integration parameters ;integrator = l-bfgs integrator = cg ;integrator = steep dt = 0.00 nsteps = 15000 periodic-molecules = yes ; center of mass removal nstcomm = 10 comm_mode = Linear ; neighbour searching nstlist = 10 ns_type = grid pbc = xyz ;periodic boundary conditions in all directions rlist = 1.5 ; electrostatics coulombtype = PME rcoulomb = 1.5 ; van der Waals interactions vdwtype = cut-off rvdw = 1.5 DispCorr = EnerPres ;tail corrections ; Ewald parameters fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-6 optimize_fft = yes ; energy minimization emtol = 10.0 emstep = 0.01 Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/periodic-surface-minimization-tp5011423.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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