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

[Tsjerk Wassenaar]

Hi,

It's not about adding points. The statistics are over all time steps
already. However, it should be noted that at t=0 the pressure was not
controlled yet. So these statistics include the convergence and are
therefore unlikely to reproduce the reference pressure. In addition, there
is the question what the distributions of average pressures over 100 ps
simulations performed at 1 bar with this compressibility and this coupling
time is, and where the observed pressure falls in this distribution. Even
then one has to realize that the tail of the Gaussian distribution is also
"normal" :) and that an average falling further out might for that matter
still be correct. For longer simulations the distribution of averages
becomes much narrower, making it easier to draw conclusions about being
converged or not.

Hope this helps,

Tsjerk
On Oct 30, 2014 7:08 AM, "Dan Sponseller" <gromacs at danpeg.com> wrote:

> 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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