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
--
========================================
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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