[gmx-users] compressing with NPT

[Elisabeth]

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
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