[gmx-users] Re: umbrella sampling with distances larger than half box size

[lloyd riggs]

Thanks,

You should make sure your WHAM is good, or your DNA isnt moving out of the box, as I watched a series of questions reply here before which showed that irrelevant WHAM data might be produced when the molecule leaves the box edges, ie you would be missing a piece or have a negative where the positive number should be in the calculations used inside WHAM.

Grüess

Stephan

-------- Original-Nachricht --------
> Datum: Mon, 25 Jun 2012 02:32:40 -0700 (PDT)
> Von: anaome <anaome at fundp.ac.be>
> An: gmx-users at gromacs.org
> Betreff: [gmx-users] Re: umbrella sampling with distances larger than half	box size

> Thanks Stephan for your suggestions,
> 
> A finally found a solution for distance larger than half the box size:
> 1) Regenerate the tpr files with pbc=no
> 2) Perform WHAM analysis with the umbrella forces (-if)
> 
> 
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