From: harish vashisth (harish.vashisth_at_gmail.com)
Date: Fri May 25 2012 - 12:43:50 CDT
Hi Jerome,
Thanks for your suggestions again. I guess you have answered my question.
I will try using colvars and tclforces together if there is no obvious
restriction for their use simultaneously.
-Harish
On Fri, May 25, 2012 at 1:17 PM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:
> In principle, the tclForces and colvars should be able to work together
> nicely.
>
> On a side note, the fact that your custom forces cause large
> translations and rotations might indicate a problem with the way they
> are defined or computed. If you are biasing the protein's
> conformation, it should be possible to do it with zero net force on
> the center of mass, and zero torque. But of course that depends on the
> specifics of your algorithm.
>
> Jerome
>
>
> On 25 May 2012 18:25, harish vashisth <harish.vashisth_at_gmail.com> wrote:
> > 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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