VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Mar 09 2010 - 04:47:13 CST

• Next message: Ajeeta kaushiki: "Re: script for area per lipid"
• Previous message: politr_at_huji.ac.il: "analyzing gromacs trajectory (.trr) with VMD"
• In reply to: politr_at_huji.ac.il: "analyzing gromacs trajectory (.trr) with VMD"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

2010/3/9 <politr_at_huji.ac.il>:
> Dear VMD users and developers.

dear regina,

> I'm trying to analyze GROMACS output trajectory (.trr) using VMD. For
> example, I'm trying to use pbcwrap in order to center my protein in the
> solvent box and nothing happens. Does anyone have suggestion? I wrote a lot
> of scripts for analyzing NAMD trajectories using VMD and I want be able to
> use them with gromacs's .trr. Is it possible?

.trr files contain coordinates and box information just as .dcd files do.
there should be no principle problems.

what version of pbc wrap do you use? the one embedded in VMD?

cheers,
    axel.

> Regina
>
>

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

• Next message: Ajeeta kaushiki: "Re: script for area per lipid"
• Previous message: politr_at_huji.ac.il: "analyzing gromacs trajectory (.trr) with VMD"
• In reply to: politr_at_huji.ac.il: "analyzing gromacs trajectory (.trr) with VMD"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]