[gmx-users] average pressure

[Justin Lemkul]

On 9/2/17 1:34 AM, Mahboobeh Eslami wrote:
> Hi all GMX usereI have a large system composed of three protein chains. I simulated it in a triclinic box. I used Parrinello-Rahman with tau-p=2  in NPT equilibration step for 1000 ps. When I checked average pressure in this step, I find an average pressure of ~ 22 bar, rather than 1 bar. I extended this step for 3000 ps but I get similar value for average pressure. Which parameter must I change to get better average pressure?Please guide meThank you so much
> 

4 ns is not a lot of time.  The error bars are significant when interpreting 
average pressure.

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

If you have fluctuations on the order of +/- a few hundred bar (which is 
likely), then your result is statistically indistinguishable from your target value.

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================