Your problem has nothing to do with barostat. There is such thing as DispCorr. I am unsure whether if should be turned on or off in case of your model. It does influence density to certain extent.
Dr. Vitaly Chaban > -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Souilem Safa > Sent: Tuesday, 7 May 2013 4:38 PM > To: Discussion list for GROMACS users > Subject: [gmx-users] simulation single molecule in water > > Dear gromacs users, > I'm simulating a single molecule in spc water. I'm using a cubic water box > which has 3.4 nm size. > I got the toplogy of my molecule via PRODRG. > After running minimization, NVT , NPT and MD for 10 ns , I checked the > density of water ,it was less than the real value (1000 kg m\S-3\N) > ,actually I got around 950. > I have checked my mdp file in the NPT step and I was wondering about tau_p > that I should use. First I used 2.0 ps with Parrinello-Rahman coupling. > After checking in gromacs archive, I found it is better to use 0.5 ps, I > have changed tau-p ,but I still have density value less than 1000. > Details of my mdp file are below : > Run parameters > integrator = md ; leap-frog integrator > nsteps = 5000000 ; 2 * 5000000 = 10000 ps, 1 ns > dt = 0.002 ; 2 fs > ; Output control > nstxout = 1000 ; save coordinates every 2 ps > nstvout = 1000 ; save velocities every 2 ps > nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps > nstenergy = 1000 ; save energies every 2 ps > nstlog = 1000 ; update log file every 2 ps > ; Bond parameters > continuation = yes ; Restarting after NPT > constraint_algorithm = lincs ; holonomic constraints > constraints = all-bonds ; all bonds (even heavy atom-H bonds) > constrained > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > ; Neighborsearching > ns_type = grid ; search neighboring grid cells > nstlist = 5 ; 10 fs > rlist = 1.0 ; short-range neighborlist cutoff (in nm) > rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) > rvdw = 1.0 ; short-range van der Waals cutoff (in nm) > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for long-range > electrostatics > pme_order = 4 ; cubic interpolation > fourierspacing = 0.16 ; grid spacing for FFT > ; Temperature coupling is on > tcoupl = V-rescale ; modified Berendsen thermostat > tc-grps = system ; two coupling groups - more accurate > tau_t = 0.1 ; time constant, in ps > ref_t = 300 ; reference temperature, one for each group, in > K > ; Pressure coupling is on > pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT > pcoupltype = isotropic ; uniform scaling of box vectors > tau_p = 0.50 ; time constant, in ps > ref_p = 1.0 ; reference pressure, in bar > compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > ; Dispersion correction > DispCorr = EnerPres ; account for cut-off vdW scheme > ; Velocity generation > gen_vel = no ; Velocity generation is off > > What should be the origin of this density difference? > looking forward to your advise > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists