Dear GROMACS experts, I am simulating a system of two disordered proteins in vacuum. I use gromacs 4.6.5. The serial simulation works fine, but when I run it in parallel (2 processors) it gives seriously pathological results.
I use particle decomposition and periodic boundary conditions, because I want to simulate a solution at a certain concentration (technically, the simulation is in vacuum, but I have included the effects of solvation in the nonbonded terms of the force field in my coarse-grained protein model). Each protein has 300 particles. I use exactly the same parameters and input files in the serial simulation and in the parallel simulation. This is the mdp file that I use: integrator = md-vv dt = 0.02 nsteps = 500000000 nstxout = 0 nstvout = 0 nstenergy = 500000 nstlog = 500000 nstxtcout = 50000 nstcomm = 1 nstcalcenergy = 1 xtc-precision = 10 rlist = 1.4 coulombtype = shift rcoulomb = 1.2 epsilon_r = 15 vdw-type = shift rvdw-switch = 0.9 rvdw = 1.2 tcoupl = andersen tc-grps = Protein tau-t = .1 ref-t = 300 Pcoupl = no refcoord_scaling = all It works perfectly in the serial simulation, but I need to make parallel simulations in order to simulate systems with many proteins. How could I solve the problem? Thank you in advance, Agusti -- 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.
