VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 30 2004 - 01:26:48 CST

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              
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