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

[Dr. Vitaly Chaban]

Sampling over 100 ps is incredibly meaningful...


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН


On Thu, Oct 30, 2014 at 6:49 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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