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
--
========================================
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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