[gmx-users] Enforced rotation of a subunit

Kay Gottschalk kay.gottschalk at weizmann.ac.il
Sun Jan 9 15:21:54 CET 2005

Hi there,

I'd like to enforce a rotation of one subunit of a larger complex with 
respect ot the rest or of a group within a protein and monitor the 
forces/energies during the rotation. Possible applications are for 
example the rotation of a helix in a helix bundle around the long axis 
of the helix or the rotation of a sidechain along the chi1. I think the 
pull code can do it in principle, but since AFM pulling invokes a 
linear movement, I'd have to pull at different atoms in different 
directions, and the directions have to be updated over time.  So far I 
failed in setting it up. A work-around would be to use some simple 
geometric modification of the original pdb-file, doing a small rotation 
with something like a perl script and than constraining the system and 
monitoring the constraint force. But I don't like that, since the 
initial rotation might screw up the system completely, making the 
results arbitrary. Do you guys have any suggestions? I assume others 
have thought of similar simulations...Thanks a lot,

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