From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri May 25 2012 - 01:11:47 CDT
why don't you just try?
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von harish vashisth
Gesendet: Freitag, 25. Mai 2012 07:06
An: NAMD list
Betreff: namd-l: queries about "Tclforces" utility in NAMD
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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