VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Mon Apr 22 2024 - 13:33:07 CDT

Thank you for the reply Roni, I made the same mistake as Charles.
I'll make sure to revisit the user guide to clarify that option.

Here's a similar script with a few more comments.

# Load new topology for mol1
set mol1 [mol new ../base/protein.psf]

# Load new topology for mol1
set mol2 [mol new ../base/protein.psf]

# Confirm their "ID" numbers
puts "Mol1: $mol1 Mol2: $mol2"

# Add trajectory to mol1
mol addfile trajectories/run.1.dcd waitfor all $mol1

# Add trajectory to mol2
mol addfile trajectories/run.2.dcd waitfor all $mol2

On Fri, Apr 19, 2024 at 10:45 PM Roni Saiba <ronis_at_imsc.res.in> wrote:

> Hi,
>
> molid is not a command. You have to put the specific molecule number
> instead of "molid $sel". The modified script may look something like
> this:
>
> Quoting CHARLES MCCALLUM <cmccallum_at_me.com>:
> set velid [mol new file.psf]
> set trajid [mol new file.psf]
> set molnum2 [molinfo index $trajid]
> mol addfile file.dcd type dcd waitfor all $trajid
>
> Regards,
> Roni
>
> > We are trying to do an analysis in a tcl script, and I’m a bit
> > confused as to how VMD acts versus how the VMD tcl command
> > documentation suggests. I want to load the veldcd and regular dcd
> > into two separate molids, but with the same psf:
> >
> > set velid [mol new file.psf] ;# molid “0” for example
> > set trajid [mol new file.psf];# molid “1” for example
> > mol addfile file.veldcd type dcd waitfor all molid $velid
> > mol addfile file.dcd type dcd waitfor all molid $trajid
> >
> > I would expect that adding the ‘molid $velid’ forces the veldcd to
> > to into the molid 0, that is, the velocity dcd. But it always adds
> > into the second molid (the top molid).
> >
> > We work around this by always ‘mol addfile…’ after each new molid
> > while it is the top:
> >
> > set velid [mol new file.psf] ;# molid “0” for example
> > mol addfile file.veldcd type dcd waitfor all molid $velid
> > set trajid [mol new file.psf];# molid “1” for example
> > mol addfile file.dcd type dcd waitfor all molid $trajid
> >
> > Or, we can explicitly set whichever one we want as the top with ‘mol
> > top $velid’. But it makes me wonder why it doesn’t work in the
> > first set of commands; the ‘molid $velid’ seems to be ignored. We
> > have tried this with actual numbers instead of variables. In other
> > words, the variables representing the molids are being set
> > correctly. When I make selections for the calculation later on,
> > setting the molid that I want (velocities or coordinates) works as
> > expected with ‘atomselect’. Clearly I’m missing something here.
> >
> > Thanks
> > Mike
> >
> > --
> > C. Michael McCallum
> > Professor
> > Department of Chemistry, UOP
> > mmccallum .at. pacific .dot. edu (209) 946-2636 v /
> > (209) 946-2607 fax
>
>
>
> 

-- 
Diego Enry B. Gomes, PhD
Department of Physics at Auburn University &
NIH Center for Macromolecular Modeling and Visualization
Leach Science Center - Ste. 3182 - Auburn, AL
dgomes_at_auburn.edu