[gmx-users] Distance for window spacing in US?

Justin Lemkul jalemkul at vt.edu
Wed Feb 20 22:46:48 CET 2013

On 2/20/13 11:01 AM, Yun Shi wrote:
> Hi Justin,
> I was not able  to find relevant posts in the archive. Any special
> keyword for searching?

I'm afraid I can't think of anything magical off the top of my head, no.

> But I wonder if it would introduce any additional error to deltaG
> calculations if I restrain the dissociation pathway to x axis, using
> pull_vecl = 1 0 0. Would the program then forcing the velocities along
> y and z axes to be zero?

No.  If you choose the restraint direction to only coincide with x, then 
restraint forces are only applied along x.  That does not mean there can be no 
motion along y and z.  You have to decide on a suitable dimension or set of 
dimensions based on the geometry of your system.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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