Hi Omer, You use a dielectric constant is 80, which means that the electrostatic interactions are screened. Perhaps that's why your density is low. Ran.
Omer Markovitch wrote: > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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