[gmx-users] Inaccurate pressure readings

[Dallas Warren]

Then something you have said isn't right.  In first email you said that
the pressure varies between -400 and +400 bar.  Now you say that the
average can vary from -1000 to +1000 bar.  If the instantaneous pressure
is varying from -1000 to +1000 bar, then that is not a real issue.
However, if the average can be from -1000 to +1000 bar, then that
definitely is.


Which one is it?

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
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. 

 

From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Denny Frost
Sent: Friday, 21 January 2011 9:23 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Inaccurate pressure readings

 

The average I calculate is not within -10 to 10, it is on the order of
-1000 to 1000

On Thu, Jan 20, 2011 at 3:11 PM, Dallas Warren
<Dallas.Warren at monash.edu> wrote:

You have a variable that is fluctuating over a range of 800+ units
(three orders of magnitude) and want the average to be 1.0?

 

It is not a problem as such.  If you can get a large enough data set of
pressure data, and it will have to be very large, then you might get it
close to one.

 

But as long the average you calculate is within may be an order of
magnitude (-10 to 10) then there is nothing to get too worried about.

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
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. 

 

From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Denny Frost
Sent: Friday, 21 January 2011 9:07 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Inaccurate pressure readings

 

I am running a variety of NPT simulations with polar, non-polar, and
ionic compounds.  Although my results for density agree well with
experimental values, the pressures I get from g_energy are off by 1 to 3
orders of magnitude.  In the log file, the pressure fluctuates around a
lot from -400 to 400 bar, which seems to be normal according to other
posts on this list, but the average (which is what g_energy gives me) is
not 1.0 bar, as I specified.  Does anyone know how to correct this
problem?

 

Pressure coupling parameters:

Pcoupl              =  berendsen

pcoupltype          =  isotropic

tau_p                   =  1.0

ref_p                   =  1.0

compressibility     =  4.5e-5


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