Re: vmd-l: Re: On-the-fly modification of tclforces script?

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 13 2015 - 19:05:34 CST

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
> >
>

-- 
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University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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