[gmx-users] average pressure of a system

[Dallas Warren]

Part answer is provided at http://www.gromacs.org/Documentation/Terminology/Pressure

Have you plotted how the pressure changes with time during your simulation?

What you will notice is that the pressure is oscillating between something like +300 bar and -300 bar.  With such large variations like that, is it not surprising that the average is not exactly 1?

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 


> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Dwey
> Sent: Wednesday, 11 September 2013 11:12 AM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] average pressure of a system
> 
> Hi All.
> 
>    I work on a simulation of a membrane protein in a model membrane
> (DPPC) with a total of 26,859 atoms.  In a step of NPT equilibration,
> my mdp file is used for a 100 ps NPT and it has a reference pressure
> of 1 bar.
> 
>  At the end of simulation,  I obtained a result of the average
> pressure of the system ( ~ -0.90 bar)  like
> 
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -----------------------------------------------------------------------
> --------
> Pressure                    -0.9049        2.6    186.304    13.8503
> (bar)
> 
> 
> I am wondering if  I should keep running this NPT process until the
> average pressure of the system reaches ~ 1.0 bar.
> 
> If so, how long ( how many steps) ?
> 
> Or should I modify mdp file  ? Can anyone provide some suggestions ?
> 
> 
> Likewise, at the end of Production MD for 1 ns, I obtained  average
> pressure (~2.23 bar)  of the system like
> 
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -----------------------------------------------------------------------
> --------
> Pressure                    2.23349        2.1     164.97    10.9381
> (bar)
> 
> Should I run a longer simulation until the average pressure reaches ~
> 1.0 bar,  although average energy, average temperature (323 K),
> average density (1022 kg/m^3) are already at  the desired values ?
> 
> How should I do to stabilize average pressure  at a desired value (~1
> bar) ?
> 
> 
> Thanks for any input.
> Dwey
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