[gmx-users] Re: compressing with NPT

[Vitaly Chaban]

Because when you introduce constraints, you change the model. Why is
it strange for you, I would ask.

Meanwhile, the difference is comparable with RMSD.


-- 
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216




> Dear experts,
>
> I have been considering effect of fixing bond lengths in my system
> (constraints= none / all-bonds) on equilibrated density using NPT runs with
> 4.5.4. I am showing two set of results for two ref pressures of 10 and 70
> bar. in case of constraints= none I had to employ a 0.5 fs timestep
> otherwise system blows up. Can you please comment why equilibrated densities
> are different for the same reference pressure? Thanks.
>
> 70 bar, all bonds constraint
> timestep 2fs
>
> Statistics over 875001 steps [ 250.0000 through 2000.0000 ps ], 2 data sets
> All statistics are over 87501 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Pressure                    70.4993      0.092    542.944   0.222707  (bar)
> Density                     625.894       0.39    11.9075   0.110708
> (kg/m^3)
>
>
> 70 bar, constraints= none
> timestep 0.5 fs
>
> Statistics over 3500001 steps [ 250.0000 through 2000.0000 ps ], 2 data sets
> All statistics are over 350001 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Pressure                    70.6207       0.11    932.219  -0.500892  (bar)
> Density                     614.451       0.55    13.7381  -0.347349
> (kg/m^3)
>
>
> ---
>
> 10 bar, all bonds constraint
> timestep 2fs
>
> Statistics over 875001 steps [ 250.0000 through 2000.0000 ps ], 2 data sets
> All statistics are over 87501 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Pressure                    10.4843      0.039    621.684  0.0156492  (bar)
> Density                     624.362          1    12.1354   -2.11725
> (kg/m^3)
>
>
> 10 bar, constraints= none
> timestep 0.5 fs
>
> Statistics over 500001 steps [ 250.0000 through 500.0000 ps ], 2 data sets
> All statistics are over 50001 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Temperature                  299.92       0.11    4.86352  -0.139097  (K)
> Density                     600.689          2    14.7597    11.6485
> (kg/m^3)
>
>
> ;        Run control
> integrator          =  md
> dt                  =  0.002         ; 0.0005 for constraints =none
> otherwise blows up
> nsteps              =  1000000
> 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
> rvdw-switch         =  0.9
>
> ;        Cut-offs
> rlist               =  1.25
> rcoulomb            =  1.0
> rvdw                =  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               =  2
> compressibility     =  4.5e-5 4.5e-5
> ref_p               =  10
>
> constraints             = all-bonds
> constraint-algorithm = lincs