From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri May 25 2012 - 11:11:23 CDT
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.
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.
> On Fri, May 25, 2012 at 3:48 AM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>
>> 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.
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