[gmx-users] Problem with pressure form g_energy

[Justin A. Lemkul]

Mikhail Stukan wrote:
>  
> 
> Dear gmx-users,
> 
>  
> 
> I have experienced the following problem with g_energy program. The 
> problem is the same for at least three versions (3.3.4,  4.0.7 and 
> 4.5.1). When I calculate pressure value (in NPT simulation) using 
> g_energy I obtain the result (average value plus errors, drift etc.) and 
> the instantaneous values of the pressure in energy.xvg file. But then, 
> if I try to calculate the average value based on these instantaneous 
> values I have significantly different number. I assume that the problem 
> could be in precision (I run double precision version of GROMACS). 
> Option  -dp in g_energy changes nothing, probably rounding is at some 
> higher level than that. Is there any way to solve this issue? Should I 
> also trust the result of g_energy rather than data in energy.xvg?  For 
> the parameters that expose minor fluctuations (volume, density, 
> temperature) this problem doesn’t occur.
> 
>  

The g_energy result is more accurate.  There are numerous discussions in the 
list archive on this topic, for example:

http://lists.gromacs.org/pipermail/gmx-users/2009-August/044542.html
http://lists.gromacs.org/pipermail/gmx-users/2006-March/020288.html

-Justin

> 
> Thank you very much in advance,
> 
> Mikhail      
> 
>  
> 
> =============================================
> 
> Dr Mikhail Stukan
> 
> Schlumberger Dhahran Carbonate Research Center,
> 
> Dhahran Techno Valley  - KFUPM,
> 
> P.O. Box 39011, Dammam / Doha Camp  31942,
> 
> Kingdom of Saudi Arabia
> 
> Tel: +966 3 331 0300 ext 6182
> 
> Fax:+966 3 330 0845
> mstukan at slb.com <mailto:mstukan at slb.com>
> 
>  
> 

-- 
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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

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