Re: queries about "Tclforces" utility in NAMD

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri May 25 2012 - 12:17:14 CDT

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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