From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri May 25 2012 - 02:48:01 CDT
On 25 May 2012 07:06, harish vashisth <harish.vashisth_at_gmail.com> wrote:
> Dear all,
> 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.
These are not part of NAMD.
> (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.
Same thing. Note that the colvars module does these things
transparently for you, if there is any chance that your custom forces
can be implemented there.
> (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..
These commands are relatively recent additions to Tcl. If you manage
to compile NAMD linked to a recent Tcl implementation (ie version
8.5), you'll have access to them.
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