[gmx-users] seeming paradox with gmx wham

Justin Lemkul jalemkul at vt.edu
Mon Mar 12 23:07:23 CET 2018

On 3/12/18 3:42 PM, Alex wrote:
> I actually understood your tutorial perfectly well. What I didn't 
> expect is such a significant dependence on direction (assuming 
> spherical symmetry clears the situation).
> I also had to use direction-periodic instead of distance in your 
> tutorial, because the box is 4 nm wide and grompp is screaming about 
> distance exceeding half-box size. I used 5.0.3 before and it was fine 
> with the 'distance' directive. I think 'direction-periodic' is also 
> wrong for spherical symmetry. So, stick with distance and increase box 
> size?
That's the easiest thing to do, yes, as long as the simulation is still 
reasonably efficient.



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

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