[gmx-users] Re: compression to study pressure effect
Vitaly Chaban
vvchaban at gmail.com
Wed Jun 1 20:57:49 CEST 2011
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)
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