[gmx-users] question of smd

[Justin A. Lemkul]

fancy2012 wrote:
> Dear GMX users,
>  
> I want to do calculations of PMF based SMD and US, for the SMD 
> calculation, first I should change the coordinates of the protein and 
> ligand, so that the orientation of the ligand is parallel with Z axis. 
> Could someone tell me how to deal with this step? Thanks very much!

No, you can pull along any vector you like.  It is sometimes convenient to align 
your pulling vector with one of the axes, but it is not required.

-Justin

> All the best,
> qinghua
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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