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

[Tsjerk Wassenaar]

Hi Agnivo,

No, I was not hinting at a running average. The average of a parameter over
a certain time is a single observation, which has a certain distribution,
with the mean equal to the population (infinite time) mean, and some
standard deviation. I have posted before about this in relation to pressure
on this list. Please search the archives.

Cheers,

Tsjerk


On Fri, Oct 31, 2014 at 9:26 PM, Agnivo Gosai <agnivogromacs14 at gmail.com>
wrote:

> Dear Users
>
> Dr. Micholas : Do you suggest that I do a longer run ? I am doing another
> NPT carrying on from the previous NPT with a Parrinello-Rahman barostat. I
> am attaching the NPT pressure and density plots , if anyone wants to have a
> look at them.
>
> Dr. Vitaly : I was thinking that my equilibration did not reach the
> reference pressure because I need to do a longer run.
>
> Tsjerk Wassenaar : Are you hinting at the running average for my pressure
> plot ? I did not plot that. I was thinking of running a much longer
> simulation and use a different barostat for another NPT simulation.
>
> Dan Sponseller : I am also thinking of a much longer simulation using small
> nstenergy value. My present value is 100.
>
> To all : If you have any comment then please share.
>
> My previous mail as reference :
>
> Dear Users
>
> I have a DNA-Protein system and I use AMBER99SB-Parmbsc0 ff in GROMACS
> 4.5.7 single precision. I use spc216 for solvation and TIP 3P water model.
>
> My earlier work flow
> 1) Topology preparation
> 2) Box , Solvation and Ions
> 3) Energy minimization - Steepest descent ( converged after 1291 steps )
> 4) NVT equilibration using a V-rescale thermostat and ref temp = 300 K
>  average temp = 299.7 K after 100 ps NVT sim. Total energy also constant
> with minimal error.
> 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
>
> *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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-- 
Tsjerk A. Wassenaar, Ph.D.