[gmx-users] Re: compression to study pressure effect

[Vitaly Chaban]

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)