COM restraint in NAMD

From: Victor Ovchinnikov (ovchinnv_at_MIT.EDU)
Date: Wed Aug 22 2007 - 10:55:56 CDT

Dear all,

I am performing Steered MD (using the TclForces interface) on a solvated
protein and would like to restrain the center of mass of the protein to
keep it from drifting.

Can any of you suggest an efficient way of doing this?

Two ways came to my mind:
1) Use FreeEnergy restrains -- specify a positional restraint on the COM
of all atoms; the problem is that (correct me if I messed up) if an atom
participates in FE restraints, it's coordinates are unavailable to
`calcforces'; in order not to include SMD atoms in the FE restraint
atoms, I'd have to come up with an elaborate selection string in
`urestraint { ... '

2) Modify the TclForces script to add a COM restraining force in
addition to the steering force;
My question here is whether doing this would slow the code
substantially, since I'd have to calculate the COM at every timestep &
loop over all of the atoms in `calcforces'

Let me know if you have suggestions/comments.



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