[gmx-users] Re: compression to study pressure effect
Vitaly Chaban
vvchaban at gmail.com
Wed Jun 1 20:59:25 CEST 2011
Either a tighter pressure coupling time...
On Wed, Jun 1, 2011 at 2:57 PM, Vitaly Chaban <vvchaban at 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)
>
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