Dear All, I have simulated a protein inside a box with water and ions. I began by minimizing my system (which has a total charge of zero), until the maximum gradient was small enough and the potential energy become negative. Then I heated it, slowly, to 300K at constant volume (using berendsen thermostat and tcoupl = 1 ps). Then I performed 500 ps NVT simulation to equilibrate the temperature, at 300K. Then, I tried to equilibrate the pressure and run NPT simulation, using Berendsen barostat (p=1, pcoupl=10) and Berendsen thermostat (T=300K, tcoupl = 0.1).
My problem is, that with the barostat & thermostat both active in the same MD run, my density drops to a very low value (at the first MD steps, the density is 1000, dropping later to 100 kg/m^3). That is- my box dimensions increase significantly (from around 6x6x6 to 12x12x12 nm^3. If I change the pressure coupling constant, the speed of the expansion changes but all simulation converged to a small density between 50-100 kg/m3. Your help is appreciated; Probably, I am not controlling the simulation like I should. I will appreciate any advice. Thank you, Omer Markovitch. I have used gromacs version 3.3.3, Here is my .MDP file for the NPT run: integrator = md dt = 0.001 nsteps = 500000 comm_grps = system nstxout = 500 nstvout = 500 nstcheckpoint = 1000 nstlog = 500 nstenergy = 500 nstlist = 10 ns_type = simple pbc = xyz rlist = 1.0 coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 epsilon_r = 80 epsilon_rf = 80 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.0 table-extension = 1 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d optimize_fft = yes tcoupl = berendsen tc-grps = system tau_t = 0.1 ref_t = 300 Pcoupl = berendsen Pcoupltype = Isotropic tau-p = 10 compressibility = 4.5E-5 ref-p = 1 andersen_seed = 815131 constraints = none
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
