Rotate two linked proteins against each other and calculate energy profile

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Tue Mar 15 2011 - 14:20:00 CDT

Hi NAMD users,

I have a homo dimer which is linked via a short peptide linker. The
two monomers are supposed to rotate more or less free against each
other.

I would like to follow the energy profile while one monomer is rotated
180 degrees to see if there is on favorite position. Something like
the energy profile when rotating the dihedral angle of an Ethane
molecule.

I already have a explicite solvent, all-atom simulation running for this system.

Now my qestions:
a) Would I use FEP for the energy profile (Use coordinates from my
simulation as start structure and as target structure take coordinates
from a SMD run where I rotate one monomer by 180 degrees)? I guess
not. Since I can't tell FEP where to go.

b) Instead of using FEP, is it possible to just run a SMD where I
rotate (rotConstraints) one monomer by 180 degree and calculate the
forces from the SMD output (like in the NAMD tutorial "Force Analysis
for Constant Velocity Pulling"
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node19.html#SECTION00064100000000000000)?

c) Is it possible to rotate a molecule using tcl forces instead of SMD?

Thanks for you help.

Cheers,
Bjoern

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