[gmx-users] Re: specifying the direction of Pull in US

Justin A. Lemkul jalemkul at vt.edu
Sat Jul 7 16:53:58 CEST 2012

On 7/7/12 12:15 AM, Raj wrote:
> Thanks for ur suggestion Justin,
> I'm facing trouble in setting that vector, actually I cant figure out how
> can i set up a vector. Is there any easier way with which i can set up a
> vector. Thanks

It can be set simply to the difference in the (x,y,z) coordinates of the COMs of 
the two groups.  You can calculate the COM position of each group with g_traj 
-ox -com -x -y -z.

Alternatively, if you use "pull_geometry = distance" and set "pull_dim = Y Y Y" 
then the pulling direction is the vector between the two groups in all dimensions.



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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