[gmx-users] NPT Simulation average pressure lower than Reference set pressure

[Agnivo Gosai]

Dear Users

I have a DNA-Protein system and I use AMBER99SB-Parmbsc0 ff in GROMACS
4.5.7 single precision.

My earlier work flow
1) Topology preparation
2) Box , Solvation and Ions
3) Energy minimization - Steepest descent
4) NVT equilibration using a V-rescale thermostat and ref temp = 300 K
 average temp = 299.7 K after 100 ps NVT sim.
5) Next is NPT sim ( with same thermostat on )

*Pressure Coupling part of npt.mdp file :*

; Pressure coupling is on
pcoupl              = Berendsen     ; Pressure coupling on in NPT, also
weak coupling
pcoupltype          = isotropic     ; uniform scaling of x-y-z box vectors
tau_p               = 2.0           ; time constant, in ps
ref_p               = 1.0           ; reference pressure (in bar)
compressibility     = 4.5e-5        ; isothermal compressibility, bar^-1
refcoord_scaling    = com


*Content of npt.log file :*

Last step --- >

 Energies (kJ/mol)
          Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    1.05446e+04    1.32866e+04    6.07202e+02    5.40636e+03    4.12184e+04
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
    1.46731e+05   -1.93498e+03   -1.23170e+06   -1.17442e+05    1.30130e+03
      Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
   -1.13198e+06    2.06576e+05   -9.25405e+05    2.99973e+02   -7.72790e+01
 Pressure (bar)   Constr. rmsd
   -5.57060e+00    0.00000e+00

*g_energy output of npt.edr :*

A)​Statistics over 50001 steps [ 0.0000 through 100.0000 ps ], 1 data sets
All statistics are over 10001 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
------------------------------
-------------------------------------------------
Pressure                    -5.5706        6.2    84.8085    38.1219  (bar)

(B)All statistics are over 10001 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
------------------------------
-------------------------------------------------
Density                     1012.13       0.55    1.87172    3.17412
(kg/m^3)


*My run parameters are :*
; Run parameters
integrator  = md                ; leap-frog integrator
nsteps      = 50000             ; 2 * 50000 = 100 ps
dt          = 0.002             ; 2 fs

My reference pressure is 1 bar , the average pressure is -5.5 bar . I
believe that the system failed to achieve the reference set pressure.


*So should I carry out the simulation for a longer time ?? Or should I use
a different barostat on the next NPT run or do it in a fresh NPT run.*

*Kindly suggest.*


Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.