From: Hamed Mortazavi (hmd.mortazavi_at_gmail.com)
Date: Wed Aug 28 2013 - 07:30:07 CDT

thanks for reply.

here is header of the patch:
# 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.

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.
>