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

[Dan Sponseller]

I would recommend 200,000 time steps to try to get accurate pressure readings. Pressure, I believe, is computed from the virial and can fluctuate a lot.

Also, adjust nstcalcenergy and nstenergy to a small number, I use 10 to get more accurate pressure readings. You should have noticed the error estimate on your pressure is 6.2. That could put your actual pressure at 1.

Dan Sponseller
PhD student
George Mason University


> On Oct 30, 2014, at 1:49 AM, Agnivo Gosai <agnivogromacs14 at gmail.com> wrote:
> 
> 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.
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