VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Aug 28 2013 - 05:05:07 CDT

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.