[gmx-users] Problem during equilibration using semi-isotropic pressure coupling

Justin Lemkul jalemkul at vt.edu
Fri Oct 12 03:14:45 CEST 2018

On 10/11/18 5:01 AM, ARNAB MUKHERJEE wrote:
> Hi Justin, Thank you very much for your reply. I would try also 
> position restrain instead of freezing. But it is still strange to me 
> why I got average pressure of 1 bar after running only for 5 ns for 
> the completely frozen finite DNA when I did isotropic pressure 
> coupling. But for the infinite frozen DNA with semi isotropic pressure 
> coupling it shows problem.

If the "problem" is that your average pressure is not exactly equal to 
the target, you don't really have a problem. Reporting pressure without 
error bars is meaningless, as the link I provided before (hopefully) 
convinces you. 1.5 ± 100 is statistically no different from 1.


-- ================================================== 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.thelemkullab.com 

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