From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 13 2015 - 20:17:53 CST
Okay. Try uf[xyz] and let me know if you need something different to
achieve whatever it is you're after.
Cheers,
John
On Sat, Nov 14, 2015 at 01:28:39AM +0000, Tristan Croll wrote:
> Only in the fact that I was ignorant of their existence, by the looks of things. Well, that makes life easier...
>
>
>
> Tristan Croll
> Lecturer
> Faculty of Health
> School of Biomedical Sciences
> Institute of Health and Biomedical Engineering
> Queensland University of Technology
> 60 Musk Ave
> Kelvin Grove QLD 4059 Australia
> +61 7 3138 6443
>
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>
>
>
> > On 14 Nov 2015, at 11:05 am, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > Tristan,
> > Since I don't have much context from the prior discussion, how does this
> > differ from setting ufx/ufy/ufz in VMD?
> >
> > Cheers,
> > John
> >
> >> On Sat, Nov 14, 2015 at 12:14:28AM +0000, Tristan Croll wrote:
> >> Something like:
> >>
> >> imd impulse <mol> <index> <force vector>
> >>
> >> as a simple wrapper for addForce would add a lot of flexibility.
> >>
> >> Cheers,
> >>
> >> Tristan
> >>
> >>
> >> ________________________________________
> >> From: Tristan Croll
> >> Sent: Saturday, 14 November 2015 8:48 AM
> >> To: Jim Phillips; namd-l_at_ks.uiuc.edu; Tristan Croll
> >> Cc: vmd-l_at_ks.uiuc.edu
> >> Subject: Re: namd-l: On-the-fly modification of tclforces script?
> >>
> >> Hi again,
> >>
> >> Before seriously getting into this, I'm thinking it would be more elegant (and long-term useful) to make Molecule::addforce (from Molecule.C) available as a TCL command in VMD. On the downside, the added forces would have to be calculated (or at least re-applied) at each step in VMD, but on the plus side there's no file i/o involved. What do you think?
> >>
> >> Thanks,
> >>
> >> Tristan
> >>
> >> ________________________________________
> >> From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Tristan Croll <tristan.croll_at_qut.edu.au>
> >> Sent: Wednesday, 11 November 2015 8:03 AM
> >> To: Jim Phillips; namd-l_at_ks.uiuc.edu
> >> Subject: Re: namd-l: On-the-fly modification of tclforces script?
> >>
> >> Thanks Jim. I'll start tinkering with that.
> >>
> >> ________________________________________
> >> From: Jim Phillips <jim_at_ks.uiuc.edu>
> >> Sent: Wednesday, 11 November 2015 1:53 AM
> >> To: namd-l_at_ks.uiuc.edu; Tristan Croll
> >> Subject: Re: namd-l: On-the-fly modification of tclforces script?
> >>
> >> Hi Tristan,
> >>
> >> In NAMD 2.11b1 you can do the following:
> >>
> >> tclForces on
> >> tclForcesScript {
> >> }
> >> startup
> >> while ( 1 ) {
> >> clearconfig ; # drop previously requested atoms
> >> source forcescript.tcl
> >> run 200
> >> }
> >>
> >> The main function of the tclForcesScript is to delay tclForces setup until
> >> after startup has progressed far enough to process atom lookup commands.
> >> You can give it /dev/null or an inline script with at least one newline as
> >> above. I could make tclForcesScript optional, but I think keeping it
> >> mandatory results in clearer error messages for new users.
> >>
> >> The "startup" command is like "run 0" without the force calculation, so it
> >> won't notice that you haven't defined a calcforces proc. Without the
> >> "startup" command you would need to do this:
> >>
> >> tclForces on
> >> tclForcesScript {
> >> proc calcforces {} { }
> >> }
> >> run 0
> >> .
> >>
> >> Note that in 2.11b1 if you want total forces on atoms/groups you need to
> >> explicitly request them. For backwards compatibility use "catch":
> >>
> >> tclForces on
> >> tclForcesScript {
> >> catch { enabletotalforces }
> >> proc calcforces {} { }
> >> }
> >>
> >> Also, since you're hoping to push updates from VMD, you at least need to
> >> use an atomic filesystem operation like rename to update forcescript.tcl
> >> so NAMD doesn't see an incomplete file, or you could use sockets. For an
> >> example see the file lib/replica/namd_replica_server.tcl in NAMD 2.8.
> >>
> >> Jim
> >>
> >>
> >>> On Tue, 10 Nov 2015, Tristan Croll wrote:
> >>>
> >>> Hi all,
> >>>
> >>>
> >>> I'm looking for a way to add some more complex interactions to interactive MD simulations (e.g. to force a defined group of atoms into a particular conformation). Preferably I'd like to be able to do this on-the-fly without having to restart the simulation. Would an approach something like the following in the NAMD configuration file work?
> >>>
> >>>
> >>> tclForces on
> >>>
> >>>
> >>> while {1} {
> >>>
> >>> tclForcesScript forcescript.tcl
> >>>
> >>> run 200
> >>>
> >>> }
> >>>
> >>>
> >>> .. with forcescript.tcl being modified/replaced as necessary from within VMD?
> >>>
> >>>
> >>> Thanks,
> >>>
> >>>
> >>> Tristan
> >
> > --
> > NIH Center for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> > http://www.ks.uiuc.edu/Research/vmd/
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/
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