[gmx-users] Distance for window spacing in US?
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users