[gmx-users] average pressure
jalemkul at vt.edu
Sat Sep 2 23:21:21 CEST 2017
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
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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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