From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Aug 28 2013 - 07:45:20 CDT

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take a lot), you would have found that this has long been superseded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.