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

[Vitaly Chaban]

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)
>