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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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