From: Hamed Mortazavi (hmd.mortazavi_at_gmail.com)
Date: Wed Aug 28 2013 - 11:03:01 CDT

Axel,
Thanks for Topotools, hint and plugin it self.

now to visualize my molecule: topotools reads original datafile and
recognizes the bonds. then I "load data into molecule" from lammps dump
file and finally change representation settings in "Graphics" tab in VMD.
what I'm wondering is whether there is a way to combine all these three
steps and not to do it for every single molecule? there might be no or an
obvious solution for this!

Cheers,

Hamed.

On Wed, Aug 28, 2013 at 2:45 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Wed, Aug 28, 2013 at 2:30 PM, Hamed Mortazavi
> <hmd.mortazavi_at_gmail.com> wrote:
> > thanks for reply.
> >
> > here is header of the patch:
>
> this is *not* a patch, but a VMD Tcl script (same as the save state
> file, btw) and - as you can see from the date - it is *very* old. if
> you had done just a little research on the web (and it doesn't really
> take a lot), you would have found that this has long been superseded
> by the topotools plugin, which offers read and write support for
> LAMMPS data file. furthermore, the description associated with this
> file - and just general common sense - should tell you, that you can
> in principle use *any* of the file formats supported by VMD to save
> the data, for as long as you can find a way to save both, coordinate
> and topology information (e.g. .psf + .dcd, .psf + .pdb, hoomd, and
> many more).
>
> > # small script to extract bonding info from a lammps data file
> > # so that VMD will display the correct bonds for CG-MD.
> > # (c) 2007 Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
> >
> > about VMD; I save coordinates then save visualization state and then try
> to
> > load them both. I assume this you meant. right? I still have same
> problem.
>
> if you want specific help, you have to be more specific in your
> description and provide a way to reproduce what is worrying you. there
> are no psychics around here, therefore just saying "it doesn't work"
> doesn't work.
>
> it sounds a lot to me, that you need to spend some more time reading
> the VMD user's guide, particularly the parts about Tcl scripting and
> also go over some of the scripting tutorials to get a better
> understanding of the processes behind the scenes. short of seeing what
> you do exactly there is little else i can do besides what i already
> told you.
>
> axel.
>
>
> >
> > On Wed, Aug 28, 2013 at 12:05 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >>
> >> On Wed, Aug 28, 2013 at 11:58 AM, Hamed Mortazavi
> >> <hmd.mortazavi_at_gmail.com> wrote:
> >> > Thanks for reply.
> >> > Actually I used your patch to extract bonding info from LAMMPS data
> >> > file.
> >> > could you help me to save new structure data file created by this
> patch?
> >> > or
> >>
> >> what "patch" are you talking about? it is impossible to give precise
> >> answers to vague descriptions.
> >>
> >> > is there a way in VMD to save this as new data file + state of
> >> > visualization?
> >>
> >> i just said there is and explained how it works. what else do you need
> to
> >> know?
> >>
> >> axel.
> >>
> >>
> >> >
> >> >
> >> >
> >> > On Wed, Aug 28, 2013 at 11:52 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> >> > wrote:
> >> >>
> >> >> On Wed, Aug 28, 2013 at 10:43 AM, Hamed Mortazavi
> >> >> <hmd.mortazavi_at_gmail.com> wrote:
> >> >> > Hi,
> >> >> >
> >> >> > to visualize my polymer molecule I run a patch on VMD to create
> bonds
> >> >> > between beads. this works well, but if I save the state and load it
> >> >> > from
> >> >> > .vmd file not only successive beads in polymer but all are shown
> >> >> > bonded
> >> >> > together. is this a mistake in patch or settings in VMD?
> >> >>
> >> >> if you save the state in VMD you save the "visualization state", you
> >> >> do *not* save the structure or coordinates. if you load the state
> back
> >> >> into VMD, it will try to re-read the original coordinate files. if
> you
> >> >> change the structure/topology and/or coordinates, you have to save
> >> >> those as well to the corresponding files (or rather make copies of
> the
> >> >> originals and then save).
> >> >>
> >> >> axel.
> >> >>
> >> >> >
> >> >> > Best,
> >> >> >
> >> >> > Hamed.
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> >> International Centre for Theoretical Physics, Trieste. Italy.
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> International Centre for Theoretical Physics, Trieste. Italy.
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>