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

[Tsjerk Wassenaar]

Oh, I mean a single observation from a certain distribution...

T.

On Fri, Oct 31, 2014 at 9:31 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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.
>
>


-- 
Tsjerk A. Wassenaar, Ph.D.