VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jan 19 2011 - 14:30:29 CST

On Wed, 2011-01-19 at 14:32 -0500, Phelan Jr., Frederick R. Dr. wrote:
> Hi,

hi fred,

> We have a job which is essentially looking at the diffusion of a
> single FENE chain using LAMMPS. The output written in .lammpstrj
> format.

> For a chain of up to about 20 units, using the drawing method CPK
> displays both the bead and the bond between the beads. However, when
> you jump to some larger number (say N=100) all of a sudden the bonds
> disappear and only beads are displayed.

hmmm... i'd like to see a couple of files that show this
inconsistent behavior. it is likely to be related to something else.

> Is there any generic nethod for making sure bonds are displayed?

the lammps dump actually does not contain _any_ bonding information.
this is created through a heuristic guess process upon loading the
trajectory, but that is very difficult to get right due to the way
how VMD guesses bonds and the lack of suitable information.

a better way to handle this is to properly read in the bonding
information from a data file using the topotools plugin.
you may need to use a VMD alpha version or download and install it
from here http://sites.google.com/site/akohlmey/software/topotools

it may be convenient to set suitable atom names other information
through some VMD/tcl scripting and then write it out the result to
a .psf, .js or similar file format, that can be read in directly
and faster by VMD.

let us know if you need help with that.

cheers,
    axel.

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> Thanks,
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> Fred
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> ______________________________________________________________________
> Frederick R. Phelan Jr., Ph.D.
> Complex Fluids Group
> Polymers Division
> National Institute of Standards and Technology
>
>
> ______________________________________________________________________
> NIST, Bldg. 224/Rm. A209
> 100 Bureau Dr., STOP 8542
> Gaithersburg, MD 20899-8542
> 301.975.6761 (VOX)
> 301.975.4924 (FAX)
> Frederick.Phelan_at_nist.gov
>
> My Polymers Home Page
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-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.