VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Apr 29 2014 - 13:37:43 CDT

On Tue, Apr 29, 2014 at 2:10 AM, Ginny arora <ginnyz678_at_gmail.com> wrote:
>
> Dear Axel,
>
> Thanks a lot for your reply.
>
> Please check where I am making mistake to plot rdf from vmd
>
> 1. I have made the psf file of input file of lammps like in.config to
> config.psf.
> 2. Then loaded config.psf file and traj.all.dcd file. in vmd.
> 3. Open tk console -> used command
> pbc wrap -compound res -all
> pbc box

there is not reason at all to do this. the rdf code will have to do
wrapping for periodic systems anyway.

> 4. Then open extensions->rdf->by default box dimensions are set in utilities
> then selection 1 name selection 2 name ar

> when click on compute g(r) it shows g(r) calc. successfull 0 frame
> processed.

well, then you either made a mistake at this last step and used the
gofr gui incorrectly or already made a mistake when loading the
trajectory. when it processes 0 frames, you operated on an "empty"
molecule. also, have you tested the selections in the GUI? do they
contain any atoms for any frames?

axel.

> Kindly suggest.
>
> Thanks and Regards
> Ginny
>
>
>
> On 28 April 2014 20:18, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Mon, Apr 28, 2014 at 1:15 AM, Ginny arora <ginnyz678_at_gmail.com> wrote:
>> > Dear All,
>> >
>> > When I load files in xyz and dcd formats in vmd to generate plot of rdf
>> > it
>> > is showing line on the x-axis only.
>>
>> please note, this is a VMD question and not a LAMMPS question and thus
>> should be posted to the VMD mailing list.
>>
>> > I tried first uploading with psf file then dcd file even then it is
>> > showing
>> > the line on xaxis.
>> >
>> > kindly suggest what may be the reason.
>>
>> impossible to say with so little information. probably, you didn't do
>> the RDF calculation correctly
>>
>>
>> >
>> > Thanks and Regards
>> > Ginny
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> > Instantly run your Selenium tests across 300+ browser/OS combos. Get
>> > unparalleled scalability from the best Selenium testing platform
>> > available.
>> > Simple to use. Nothing to install. Get started now for free."
>> > http://p.sf.net/sfu/SauceLabs
>> > _______________________________________________
>> > lammps-users mailing list
>> > lammps-users_at_lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/lammps-users
>> >
>>
>>
>>
>> --
>> 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.