From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 30 2004 - 13:10:34 CST

Hi,
  While we're on the subject of LES, I thought it'd be useful to
forward Jordi's comments about what he does when viewing NAMD-based LES
simulations in VMD:

----- Forwarded message from Jordi Cohen <jordi_at_ks.uiuc.edu> -----

Date: Fri, 30 Jan 2004 11:42:55 -0600 (CST)
From: Jordi Cohen <jordi_at_ks.uiuc.edu>
cc: "Matthew C. Lee" <mattlee_at_udel.edu>, vmd_at_ks.uiuc.edu
Subject: Re: vmd-l: Does VMD support LES simulations?

Hi,

I use VMD to view LES trajectories (created by NAMD). Neither the
coordinate trajectories or the structure files contain any information
that can distinguish between different LES copies (except by their index).
So initially, I can see all the copies, but I can't distinguish between
them.

In my case, I need to load a separate PDB of my system that has different
values of the beta column (or occupancy) for each LES copy, in the same
molecule as the trajectory. This step will assign a different beta value
to each copy. I can then use this information to distinguish between
copies. For example, coloring by beta value would color each copy
differently, and I can target a copy via atom selections using, e.g,
"resname XXX and beta 3" .

Cheers,
Jordi

On Fri, 30 Jan 2004, John Stone wrote:
>
> Matthew,
> Can you post your trajectory so I could download it? At present I don't
> have any test datasets for Amber 7 that have LES turned on, so that would
> be very helpful.
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Fri, Jan 30, 2004 at 09:06:19AM -0500, Matthew C. Lee wrote:
> > Hi, John,
> >
> > I have LES trajectory in AMBER 7 format. When you figure out the scripts,
> > could you please post a copy either on VMD website or here? I'd love to
> > have these functionalites in VMD.
> >
> > Thanks :-)
> > -- mlee
> >
> > ----- Original Message -----
> > From: "John Stone" <johns_at_ks.uiuc.edu>
> > To: "Vlad Cojocaru" <Vlad.Cojocaru_at_mpi-bpc.mpg.de>
> > Cc: "VMD" <vmd-l_at_ks.uiuc.edu>
> > Sent: Friday, January 30, 2004 2:26 AM
> > Subject: Re: vmd-l: Does VMD support LES simulations?
> >
> >
> > >
> > > Dear Vlad,
> > > Which simulation package are you using with LES? (Amber, NAMD, etc?)
> > > I took a quick read through the MOIL-View manual to see what specific
> > > features they have for viewing LES simulation results, and it looks like
> > > the main things it does are:
> > > 1) select atoms ("pick" in their docs) by LES instance-ID ("copy
> > number")
> > > 2) color by LES instance-ID ("copy number" as they say)
> > > 3) measure positional variance of the LES instances so one can determine
> > > what parts of the structure are well converged or not
> > > Is there anything else?
> > >
> > > Depending which package your using for your LES simulations and what
> > > file formats your writing, it should in principle be possible to do
> > > all of this in VMD with a bit of scripting. The big question is how
> > > the LES instances are stored in the trajectories, and whether there's
> > > enough information in there to automate most/all of that.
> > >
> > > If you've already got some data you want to visualize, I'd be willing
> > > to have a looksee at your files and give you some suggestions on doing
> > > the items above.
> > >
> > > Thanks,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > >
> > > On Thu, Jan 29, 2004 at 06:17:28PM +0100, Vlad Cojocaru wrote:
> > > > Dear VMD users,
> > > > Does anyone have experience in using VMD for Locally Enhanced Sampling
> > > > Simulations?
> > > > It would be nice to use VMD (and not MoilView...that is only for SGIs)
> > > > because I am running on a Linux platform
> > > > Thank you very much
> > > > vlad
> > > >
> > > > --
> > > > Vlad Cojocaru
> > > > Max Planck Institute for Biophysical Chemistry
> > > > Department: 060
> > > > Am Fassberg 11, 37077 Goettingen, Germany
> > > > tel: ++49-551-201.1327
> > > > e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
> > > > home tel: ++49-551-9963204
> > > >
> > > >
> > >
> > > --
> > > NIH Resource for Macromolecular Modeling and Bioinformatics
> > > Beckman Institute for Advanced Science and Technology
> > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>

----- End forwarded message -----

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078