Hi, As mentioned in the reference below, changing rlist to 1.4 (greater than the nonbonded cutoffs) and changing nstlist to 5 appears to solve the problem.
1. Siewert J. Marrink et al., “Comment on “On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models” by M. Winger, D. Trzesniak, R. Baron and W. F. van Gunsteren, Phys. Chem. Chem. Phys., 2009, 11, 1934,” Physical Chemistry Chemical Physics 12, no. 9 (2010): 2254. On Tue, Jun 15, 2010 at 10:44 PM, Michael Lerner <[email protected]> wrote: > Hi, > > I want to run some MARTINI DPPC/water simulations using the microcanonical > (NVE) ensemble. > > I ran a long NVT simulation to make sure things were fully equilibrated. > Then I took the .gro file as input and removed the temperature/pressure > coupling options from my .mdp file. I also removed the > center-of-mass-removal options. Unfortunately, the temperature decreases > rather quickly from 323K to below 200K. I've included my .mdp file below. Is > there something obviously wrong with it? If not, are there other things I > should try? > > Thanks, > > -Michael > > P.S. I recently changed the email address that I use to subscribe to > gmx-users. My apologies if this gets sent to the list twice as part of that. > > Pcoupl = no > DispCorr = No > gen_vel = no > integrator = md > nstvout = 100000 > epsilon_surface = 0 > nstlog = 2500 > nstenergy = 2500 > comm_mode = None > xtc_precision = 100 > rvdw_switch = 0.9 > epsilon_r = 15 > nstxtcout = 2500 > ewald_rtol = 1e-05 > continuation = yes > constraints = none > nsteps = 500000 > vdw_type = Shift > tcoupl = no > rlist = 1.2 > lincs_warnangle = 30 > xtc-grps = Prot > lincs_order = 4 > dt = 0.02 > tinit = 0.0 > coulombtype = Shift > shake_tol = 0.0001 > nstlist = 5 > rcoulomb_switch = 0.0 > morse = no > nstxout = 100000 > annealing = no > constraint_algorithm = Lincs > pbc = xyz > rcoulomb = 1.2 > compressibility = 5e-5 5e-5 > energygrps = Prot SOL > ns_type = grid > nstfout = 0 > rvdw = 1.2 > > -- > Michael Lerner, Ph.D. > IRTA Postdoctoral Fellow > Laboratory of Computational Biology NIH/NHLBI > 5635 Fishers Lane, Room T909, MSC 9314 > Rockville, MD 20852 (UPS/FedEx/Reality) > Bethesda MD 20892-9314 (USPS) > -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS)
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
