[gmx-users] Inaccurate pressure readings

[Justin A. Lemkul]

Denny Frost wrote:
> from -1000 to 1000, depending on the system.  The simulation box is 
> 8x8x8 nm (roughly) and contains about 12,000 atoms
> 

Are the systems even stable?  Is there a trend in the pressure, or is it stable 
at those values?  It seems that the systems are either exploding or imploding. 
How long are the simulations?  Can you post a complete .mdp file?

-Justin

> On Thu, Jan 20, 2011 at 3:09 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Denny Frost wrote:
> 
>         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?
> 
> 
>     What is the average value you're getting?  How long are your
>     simulations?
> 
>     -Justin
> 
> 
>         Pressure coupling parameters:
>         Pcoupl              =  berendsen
>         pcoupltype          =  isotropic
>         tau_p                   =  1.0
>         ref_p                   =  1.0
>         compressibility     =  4.5e-5
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================