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

[Justin A. Lemkul]

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

-- 
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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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