How do you keep atoms a fixed distance apart?

Date: Wed Nov 26 2008 - 00:59:47 CST


I'd like to run a simulation in which 2 atoms are kept a certain distance
apart (not fixed in space). I've searched the NAMD and VMD mailing list
archives and haven't found anything helpful. As far as I can tell, NAMD
has no built-in protocols to do this so I'm planning on using a .tcl
script. Does anyone know if such a script has already been written or how
one would go about writing it? I know the SHAKE algorithm is used to keep
waters rigid so is there a way to make use of SHAKE in a .tcl script?



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