From: harish vashisth (harish.vashisth_at_gmail.com)
Date: Fri May 25 2012 - 10:06:39 CDT
Hi Jerome,
Thanks a lot for your suggestions. I think your colvars idea is very
helpful. I looked at the "component orientation" which can be used to
remove net translation/rotation of protein per these lines in the user's
guide:
*Hint: stopping the rotation of a protein.* To stop the rotation of an
elongated macromolecule in solution (and use an anisotropic box to save
water molecules), it is possible to define a colvar with an
orientationcomponent, and restrain it throuh the
harmonic bias around the identity rotation, (1.0, 0.0, 0.0, 0.0). Only the
overall orientation of the macromolecule is affected, and *not* its
internal degrees of freedom. The user should also take care that the
macromolecule is composed by a single chain, or disable wrapAll otherwise
However, my another concern is that even if I use colvars to remove net
translation/rotation of my protein on-the-fly, I still need to use
"tcl-forces" to apply the force I want. is it allowed in parallel runs to
use two force-updates like in colvars as well as from calcforces. Some
people in the past have experienced these issues as i looked in the mailing
list, but did not see a solution to them. Any suggestions you might provide
may be helpful.
Regards,
-Harish
On Fri, May 25, 2012 at 3:48 AM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:
> Hi Harish,
>
> 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.
>
> Best,
> Jerome
>
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