From: harish vashisth (harish.vashisth_at_gmail.com)
Date: Fri May 25 2012 - 00:06:28 CDT
I've been trying to use "tclforces" utility to add some external
forces to a protein. I have used tclforces successfully in the past, but
have following questions for what I am trying to carry out now:
(a) Under tclforces, do we have access to transformation matrix routines
similar to vmd, which can be used on-the-fly to align particular atoms in
an NAMD run? Specifically, my protein diffuses during the simulation and
the way I am applying forces, either I have to remove net
translation/rotation of my protein in a running simulation or if I want to
skip that, I need to align a target structure on-the-fly to compute my
force direction vector.
(b) related to (a)--is it possible to use "measure fit" vmd command under
tclforces. I guess not as vmd routines have no direct relation to NAMD's
source unless someone has implemented them under tcl-interpreter of NAMD
similar to commands like vecsub, vecadd etc.
(c) it also appears that NAMD's tcl-interpreter does not understand tcl
commands: lassign, lvarpop...or am I missing something?..I have tried these
things on a serial binary of version 2.8/2.9..
Any suggestions from more experienced users/developers would be helpful.
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