[gmx-users] Pressure change after NPT equilibriation

[Justin A. Lemkul]

shilpa yadahalli wrote:
> After doing NPT simulation I plot pressure and density. How much 
> pressure change is considered as normal? I'm getting pressure change +/- 
> 500 bar, after doing NPT equilibration for most of my proteins. And for 
> one of the protein it is as high as +/- 1000 bar.
> Can anybody tell me what is the Normal/expected pressure change. My 
> temperature is constant 300 K. (I m running simulations at normal 
> conditions of temperature and pressure. 300K, 1 bar, using  _AMBER99SB_ 
> FF, protein is globular with 92 amino acids). Log file etc, does not 
> shows any warnings and simulation also does not show any inconsistent 
> topology shifts.
> After my production run also, i do not get any warnings. and my rmsd is 
> below 0.2.
> but i am not much happy with the pressure changing so much.
> 

Sounds completely normal.

http://www.gromacs.org/Documentation/Terminology/Pressure

You haven't shown your .mdp settings so it's hard to gauge what you should 
expect, but again, this is expected behavior for the reasons described at the 
above link.

-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

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