Dear all, 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)
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