VMD-L Mailing List

From: Hamed Mortazavi (hmd.mortazavi_at_gmail.com)
Date: Wed Aug 28 2013 - 04:58:32 CDT

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
is there a way in VMD to save this as new data file + state of
visualization?

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.
>