From: harish vashisth (harish.vashisth_at_gmail.com)
Date: Fri May 25 2012 - 11:25:10 CDT
Thanks, Jerome. Actually, I have a "tclforces" implementation, which works
fine. Bue due to the external forces I am applying, the protein
rotates/translates a lot more than what it usually does in an MD run. All I
want is to remove that net draft (translation/rotation) due to additional
tcl-forces. Meaning, I cannot re-implement the "tclforces" code in colvars,
but can i use colvars to remove translation/rotation in combination with
whatever my "tclforces" routines do? Please let me know I could not get my
point across..Thanks again for your time.
Regards,
-Harish
On Fri, May 25, 2012 at 12:11 PM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:
> The point of my question was, whether you could implement your custom
> force entirely within the colvars module. Not knowing what you are
> trying to do, I can't tell.
>
> Best,
> Jerome
>
> On 25 May 2012 17:06, harish vashisth <harish.vashisth_at_gmail.com> wrote:
> > 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 orientation
> > component, 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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