Either a tighter pressure coupling time...
On Wed, Jun 1, 2011 at 2:57 PM, Vitaly Chaban <vvcha...@gmail.com> wrote: > Hmm... > > > 1. The background of the task is not quite clear for me. > > 2. Evidently, the fluctuations are higher than the difference for your > pressures. > > 3. Why not to use significantly larger systems and significantly > larger difference between pressures? > > > > -- > Dr. Vitaly V. Chaban, Department of Chemistry > University of Rochester, Rochester, New York 14627-0216 > > > > >> >> I am trying to study the effect of pressure on total potential of my system >> (8 polymer chains). My problem is that I dont see a systematic effect of >> pressure on potentials and I cant judge if different pressures increase or >> decrease potential. This is the critical observable in my system and with >> high fluctuations I am getting I cant make comment on pressure effect. Total >> drift is high in most potential functions..I start my runs from a frame >> which is the output of an older NPT run (I use cpt file) that has a close >> density to what I want. In the production runs (NPT for 12 27 70 bar). >> >> Below is the settings I am using and I really appreciate it if you could >> comment on the most important factors for such a study. I tried different >> cutoffs as well...I though maybe increasing cutoffs invloves more >> interactions and can represent better the pressure effect... >> >> Thanks so much! >> >> >> ; Run control >> integrator = md >> dt = 0.002 >> nsteps = 1000000 ;5000 >> nstcomm = 100 >> >> ; Output control >> nstenergy = 100 >> nstxout = 100 >> nstvout = 0 >> nstfout = 0 >> nstlog = 1000 >> nstxtcout = 1000 >> >> ; Neighbor searching >> nstlist = 10 >> ns_type = grid >> >> ; Electrostatics/VdW >> coulombtype = Shift >> vdw-type = Shift >> rcoulomb-switch = 0.5 ;0 >> rvdw-switch = 0.9 ;0 >> >> ; Cut-offs >> rlist = 1.32 ;1.25 ; tired different >> cutoffs and r -switch... >> rcoulomb = 1.1 ;1.0 >> rvdw = 1.1 ;1.0 >> >> ; Temperature coupling >> Tcoupl = v-rescale >> tc-grps = System >> tau_t = 0.1 >> ref_t = 300 >> >> ; Pressure coupling >> Pcoupl = Parrinello-Rahman >> Pcoupltype = isotropic >> tau_p = 1 >> compressibility = 3.5e-5 >> ref_p = 10 >> >> ; Velocity generation >> gen_vel = no;yes >> gen_temp = 300.0 >> gen_seed = 173529 >> >> ; Bonds >> >> constraints = all-bonds >> constraint-algorithm = lincs >> >> >> results for 12 27 70 bar resp. >> >> >> Statistics over 2043101 steps [ 500.0000 through 4586.2000 ps ], 17 data >> sets >> >> All statistics are over 204311 points >> >> >> >> Energy Average Err.Est. RMSD Tot-Drift >> >> ------------------------------------------------------------------------------- >> >> LJ (SR) -634.358 2.9 11.0696 -20.3551 >> (kJ/mol) >> >> Coulomb (SR) 184.082 1.4 3.62712 9.04046 >> (kJ/mol) >> >> P*otential 642.528 6.4 23.1897 -44.6636 >> (kJ/mol)* >> >> Kinetic En. 904.294 0.075 16.2742 0.382223 >> (kJ/mol) >> >> Total Energy 1546.82 6.3 28.6865 -44.2813 >> (kJ/mol) >> >> Temperature 300.186 0.025 5.4023 0.126881 (K) >> >> Pressure 12.3856 0.89 887.501 5.41599 (bar) >> >> Density 824.417 2.1 9.27838 14.7965 >> (kg/m^3) >> >> >> >> >> >> Statistics over 750001 steps [ 500.0000 through 2000.0000 ps ], 17 data sets >> >> All statistics are over 75001 points >> >> >> >> Energy Average Err.Est. RMSD Tot-Drift >> >> ------------------------------------------------------------------------------- >> >> LJ (SR) -638.643 4.3 12.0718 -10.2094 >> (kJ/mol) >> >> Coulomb (SR) 184.51 1 2.89777 5.99117 >> (kJ/mol) >> >> *Potential 634.902 5.7 22.2857 -21.4761 >> (kJ/mol)* >> >> Kinetic En. 904.181 0.11 16.2261 -0.275076 >> (kJ/mol) >> >> Total Energy 1539.08 5.7 27.9661 -21.7511 >> (kJ/mol) >> >> Temperature 300.148 0.035 5.38636 -0.0913135 (K) >> >> Pressure 27.6467 1.4 881.409 8.58275 (bar) >> >> Density 826.734 3.4 9.76089 6.06824 >> (kg/m^3) >> >> >> >> >> >> 70 bar run >> >> >> even 6 ns runs gives large total drifts..e.g.13.4934 for density.. >> >> >> >> Statistics over 2750001 steps [ 500.0000 through 6000.0000 ps ], 17 data >> sets >> >> All statistics are over 275001 points >> >> >> >> Energy Average Err.Est. RMSD Tot-Drift >> >> ------------------------------------------------------------------------------- >> >> LJ (SR) -639.206 3.7 11.6741 -23.7773 >> (kJ/mol) >> >> Coulomb (SR) 182.97 1.7 4.18663 11.8694 >> (kJ/mol) >> >> *Potential 640.114 7.5 24.9191 -51.8187 >> (kJ/mol)* >> >> Kinetic En. 904.3 0.074 16.2887 0.161695 >> (kJ/mol) >> >> Total Energy 1544.41 7.5 30.1347 -51.657 >> (kJ/mol) >> >> Temperature 300.187 0.024 5.40713 0.0536754 (K) >> >> Pressure 69.7658 0.86 893.933 -2.29885 (bar) >> >> Density 829.657 2.3 8.98849 13.4934 >> (kg/m^3) > -- 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
