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

[Dallas Warren]

Here's a couple of plots to show the sort of fluctuations you can get.
How much it fluctuates depends on the systems and simulation setting,
but it should give you an idea.

https://twitter.com/dr_dbw/status/968624615063937025
https://twitter.com/dr_dbw/status/968625462959210496

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.



On Fri, 12 Oct 2018 at 12:14, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> 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
>
> -- ================================================== 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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