VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Sep 14 2006 - 16:39:36 CDT
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On 9/14/06, Robert Hoy <robhoy_at_pha.jhu.edu> wrote:
> Hi. I just started using VMD today, so apologies if I'm too green. I
there is a _ton_ of tutorial material on the VMD homepage and
other pages it refers to. you should take the time and go through
some of it. it will automatically answer a lot of beginner's questions
before they even come up.
> am trying to use VMD to display configuration files from the LAMMPS
> molecular dynamics package. I can easily convert the config files to
> .xyz files, and view the atoms as points, so that's fine. The problem
.xyz is about the worst file format to try.
since it provides no additional information.
> comes in with displaying the bonds. I am displaying bulk linear
> polymers, so each bead should have 2 bonds (or 1 if it's a chain end).
> The .xyz file does not contain bond information, so it tries to infer
> the bonds from a distance search. It gets the bonds all wrong - I get
> error messages like
>
> Info) Determining bond structure from distance search ...
> ERROR) vmdgridsearch1: exceeded pairlist sanity check, aborted
> ERROR) MolAtom 171297: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 171298: Exceeded maximum number of bonds (8).
no surprise.
> So, I need a way to give VMD the bond topology. How can I do this most
> simply?
since your system is somewhat unusual, yet you should have the best
knowledge about it, writing a small program, that creates a .psf file, is
probably the best option. the .psf file can be very minimalistic an only
contain the information you want to feed into VMD.
> Another thing I need to do is give different chains different colors.
> I know Raster3D takes a RGB triplet for each plotted point. Is there
> any way do input color information similarly in VMD?
if you create a psf file, you can assign residue names, charges etc.
then you can use the various colorization schemes integrated in VMD.
have a look at the manual for details.
cheers,
axel.
>
> Thanks,
> Robert Hoy
>
>
-- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
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