VMD-L Mailing List

From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Mon Aug 08 2005 - 14:48:05 CDT

Bob,

I am not familar with GROMACS trajectory files. However, I usually load
my .psf (Protein Structure File) into VMD, and then I load the pdb or dcd
trajectory file. For NAMD, the .pdb file does not require anything about
the connectivity. This can be included in .pdb files and perhaps VMD
reads this. However, the bond information is also in the .psf file, which
VMD reads I believe. Maybe someone else can clarify along these lines.
NAMD trajectory files do not include any information about the
connectivity, so VMD assigns bonds I believe just spatially.

Do you have a .psf file you could also load into VMD to try along with the
trajectory?

Josh

On Mon, August 8, 2005 11:42 am, Bob Johnson wrote:
>
> Hello,
> I am doing some simulations in GROMACS with carbon nanotubes. Initially
> VMD
> recognizes the C-C nearest neighbors and draws bonds between them.
> However,
> when I view the trajectory generated by GROMACS VMD no longer draws the
> bonds.
> In addition to a trajectory, GROMACS generates a restart file that
> contains the
> last frame of simulation. When I view this restart file in VMD, the bonds
> are
> drawn. Do es anyone know how to visualize the bonds throughout the whole
> trajectory and why VMD doesn't draw them in automatically?
> Thanks,
> Bob Johnson
> University of Pennsylvania
>

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Joshua D. Moore
Graduate Student
North Carolina State University
Department of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC 27695-7905
Phone: (919) 513-2051
Fax: (919) 513-2470
Email: jdmoore_at_unity.ncsu.edu
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