[gmx-users] Pressure change after NPT equilibriation

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 15 19:32:52 CET 2011

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.


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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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