[gmx-users] Inaccurate pressure readings

[Denny Frost]

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

On Thu, Jan 20, 2011 at 3:09 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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