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

[Erik Marklund]

Why not use distance pulling? Then the pull_vec is defined by the vector separating the two pull groups.

Best,

Erik

6 jul 2012 kl. 08.21 skrev Raj:

> Hi all,
> 
> I am working on steered molecular dynamics and In that I would like to pull
> the ligand ( already in complex with protein) away from the reference amino
> acid ( which I've selected so that I can direct the ligand to get closure to
> my desired amino acid residue). Now the thing is when I used VMD to assign
> the direction, The desired direction of mine is not along the proper x, y,
> or in Z axis. So my question is how can i specify the direction in a
> situation like this. I've seen in other discussions people have used
> pull_vec. How can I get the values of the pull_vec. Kindly help me . thanks
> in advance 
> 
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html