Hi all, I¹m trying to equilibrate a Martini CG simulation from an initial atomistic structure. Eq and Fc values were derived using an atomistic system. I¹ve started the dt at 0.0005 for 600000 steps, moving through 0.001, 0.0015 and 0.002 for the same number of steps, using the .mdp details below (with the exception of the time step and the output delimiters - the remaining settings are from the Martini website). During these steps the temperature dropped from approx 60000K down to 310K and the potential energy dropped from positive figures down to around -1.4*10^6. A final 600000 steps with dt = 0.002 showed a converged temp, pressure, volume, potential energy (and total energy), and very little change in the unit dimensions.
I now want to move the time step up to 0.025. I¹ve tried various dt values (0.005, 0.01, 0.015Š 0.025) using the below setup, but each time dt causes almost immediately structural explosion. The temperature and the pressure rockets up. I changed the pressure coupling to berendsen and the same happens. I have been through dozens of tau_p and tau_t combinations, each one yields a trajectory of varying length before exploding (the protein Œexplodes¹ at the exact time the the pressure and temperature increases). I have also changed the thermostat to berendsen and Nose-Hoover, using a range of 5*(dt*nsttcouple) and 20(dt*nsttcouple), respectively. I would appreciate any thoughts or suggestions on how to solve my temperature/pressure problem when I try increasing the dt to a CG value. Thanks Anthony title = Martini integrator = md dt = 0.025 nsteps = 300000 nstcomm = 100 nstxout = 10000 nstvout = 10000 nstfout = 0 nstlog = 1 nstenergy = 1 nstxout-compressed = 0 compressed-x-precision = 0 ;compressed-x-grps = energygrps = collagen solvent cutoff-scheme = Verlet nstlist = 20 ns_type = grid pbc = xyz verlet-buffer-tolerance = 0.005 coulombtype = PME ;reaction-field rcoulomb = 1.1 fourierspacing = 0.16 ;0.2 ;0.12 epsilon_r = 15 ; 2.5 (with polarizable water) epsilon_rf = 0 vdw_type = cutoff vdw-modifier = Potential-shift-verlet rvdw = 1.1 tcoupl = v-rescale ;berendsen ;v-rescale tc-grps = collagen solvent tau_t = 0.4 0.4 ;2.0 2.0 ref_t = 310 310 Pcoupl = parrinello-rahman Pcoupltype = semiisotropic tau_p = 12.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422 compressibility = 4.5e-5 0 ref_p = 1.0 1.0 refcoord_scaling = com gen_vel = no gen_temp = 310 gen_seed = 473529 continuation = yes constraints = none constraint_algorithm = lincs lincs-warnangle = 45 lincs-order=18 lincs-iter=4 -- 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.