Re: [gmx-users] simulation single molecule in water
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= 500; 2 * 500 = 1 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 listgmx-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 listgmx-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 listgmx-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
RE: [gmx-users] simulation single molecule in water
It would be better if you run it a bit longer than 10ns and check the density again. But it is not a big problem I guess as the density of water at 300K should not be exactly 1000kg/m^3. Its ~1000kg/m^3 at 277K. do not expect to get exactly real value :) Additionally your system is not purely water molecules in a box there is a small molecule in it which might have an effect on the density. Cheers, -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= 500; 2 * 500 = 1 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 listgmx-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 listgmx-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
