VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Mar 20 2014 - 11:58:09 CDT

On Thu, Mar 20, 2014 at 11:05 AM, T K <physics.usersim_at_gmail.com> wrote:
> Hello Axel
> Thank you for the quick replay, What I did was just save a LAMMPS restart
> each time step I want to visualize and then loop over all the files and
> load them into VMD, export them to file and animate that. but I think that
> is very inefficient. I wonder if there is an option to group all of the
> different
> frames that I load into one molecule file, and how will VMD handle it that
> each frame has a different number of bonds ?

as i explained before, this is not possible. you can only have
different bond topologies for different "molecules" (in VMD-speak).
the multimol animation extension, can do a movie of those.

> Also one more thing that I cant figure out is why after the first frame that
> I animate the atoms become colored red.

this is likely due to an obscure bug in the VMD internal data
structures. i've seen it many times, but have not been able to track
it down properly. you should try using a recent alpha test version of
VMD to check, if this still happens. the topotools code is ok, but it
depends on an otherwise rarely used feature (and thus not so well
tested) of VMD.

axel.

> I attach my tcl script that I use to do this.
> Thank you very much
> Taj
>
> *-------------input--------------------
> display backgroundgradient on
> for {set i 8000 ; set j 0 } {$j<1000} {incr i 628 ; incr j } {
> puts "I inside loop as $j"
> topo readlammpsdata data.${i} bond
> animate style Loop
> display resetview
> animate dup frame now $j
> mol rename $j {data.${i}}
> mol reanalyze $i
> mol color Name
> mol representation Lines
> mol selection all
> mol material Opaque
> mol addrep $j
> display resetview
> menu graphics off
> menu graphics on
> mol modstyle 0 $j VDW 0.500000 12.000000
> ##mol color Name
> mol representation VDW 2.500000 12.000000
> mol selection all
> mol material Opaque
> mol addrep $j
> mol modselect 1 $j type 2
> mol modstyle 1 $j VDW 4.000000 12.000000
> ##mol color Name
> mol selection type 2
> mol material Opaque
> mol addrep $j
> mol modstyle 2 $j Bonds 1.000000 12.000000
> ##mol color Name
> mol representation Bonds 1.000000 12.000000
> mol selection type 2
> mol material Opaque
> mol addrep $j
> mol modselect 3 $j all
> menu render off
> menu render on
> render snapshot vmdscene${j}.tga
> mol delete $j
> }
> quit
>
>
> On Sun, Mar 9, 2014 at 10:37 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Sun, Mar 9, 2014 at 7:52 AM, T K <physics.usersim_at_gmail.com> wrote:
>> > Dear VMD mailing list
>> > I am pretty new to using VMD so excuse me if this questions is a silly
>> > one.
>> > I have a simulation with a changing number of bonds which I want to
>> > visualize but cannot do so with DynamicBonds.
>>
>> why not?
>>
>> > My simulation is run on lammps
>> > so what i tried to do is simple write a datafile withe write_data and
>> > then
>> > loop over all the data files load them and create an imagefile,
>> > afterwards
>> > to animate them using an external program. But I am guessing there is a
>> > much
>> > easier way to do it completely in VMD ?
>>
>> depends. in general, VMD assumes that your bonds don't change. if they
>> do, you have to use some tricks. those tricks usually require some
>> tinkering and often some scripting, and not everything will work
>> exactly as if your bonds would not change.
>>
>> you can also do the same kind of visualization from inside LAMMPS
>> using the dump image command and automagically create an animation
>> using dump movie. that is assuming that you do have bond information
>> present, of course.
>>
>> > Hope you can help me, thank you !
>> >
>> > Taj
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.