[gmx-users] Inaccurate pressure readings

Dallas Warren Dallas.Warren at monash.edu
Thu Jan 20 23:11:21 CET 2011

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


Pressure coupling parameters:

Pcoupl              =  berendsen

pcoupltype          =  isotropic

tau_p                   =  1.0

ref_p                   =  1.0

compressibility     =  4.5e-5

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