VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Aug 06 2013 - 06:02:42 CDT

On Tue, Aug 6, 2013 at 2:00 AM, Sumit Kumar
<sumit.iocl.chennai_at_gmail.com> wrote:
> Hello Experts,
>
> I have my own coarse-grained code and I want to visualize polymer chains
> (coarse-grained FENE model) using VMD. I actually want to create movies
> using VMD. Currently, my code generates LAMMPS trajectory files which I use
> for creating videos using videomach software. The bonds are connected
> randomly and I have to remove all of them. Now what my video is left with is
> the beads moving all around - I am using LEES-Edward BC in my code. The
> beads representations don't seem good so I thought line representation will
> look better than beads representation. Can I create animations using PBD
> file alone. What else is required if I want to create animation using PDB
> file? In PDB, there is a command 'CONECT' in which you can specify the beads
> to be connected by bond but can I create animations using this PDB file, how
> do I introduce frame?

PDB files have many disadvantages and should be avoided, if possible.

in general, there are two main issues to point out:
1) vmd expects that the bonding topology remains unchanged over the
course of a trajectory, so it is read and stored only once. that
means, you can best handle this through two separate file types: one
for the topology and one with only the trajectory information.

2) the best way to communicate topology information to VMD is to use a
topology file format like .psf. the .psf format has a few variants and
is somewhat fortran centric, which may be confusing to some. but it
can also be generate with scripting, e.g. the psfgen or topotools
plugins.

> If you have any better suggestions, and if any particular file format is
> recommended, would you mind attaching those simple file formats so that I
> could modify my code accordingly?

most file formats in molecular simulations are created 'ad hoc', so
there is not much documentation outside of reading the code that
produces them. example files are useless, without information about
the formatting rules.

information about plugins shipped with VMD are here:
http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/
and - of course - in the respective source code itself. please help yourself.

axel.

> Thanks and Kind Regards
> Sumit Latiyan
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.