VMD-L Mailing List
From: Dudo (dudomail_at_gmail.com)
Date: Wed Jan 12 2011 - 12:16:39 CST
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- In reply to: Axel Kohlmeyer: "Re: VTF trajectory from coarse grained ESPReSo simulations. Visualization in Windows."
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Dear Axel,
my post wasn't intended as a complaint at all. Rather I meant to provide a
solution.
It's may be I'm new to using vmd mailing list. I'm providing additionally
the link to
the thread concerning the problem with .VTF in windows:
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/15575.html
The author of the code in fact answered to the discussion, however, the
message of his
post can be comprehensed in the following sentence:
'I have never used VMD on Windows, so I cannot say much more on that.'
Hence I have provided an easy at hand solution which works for me, and
perhaps others
may find it usefull too.
The problem with VTF (and related formats VSF, VCF) has been specified in my
previous post.
Once again, I can say in simple words that the trajectory which works in
Linux compilation
of VMD causes a crash down of VMD in Windows.
Concerning your further suggestions I agree it can be done in a handfull of
ways.
It's computers.
Best regards,
Dudo
On Wed, Jan 12, 2011 at 6:40 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> dudo,
>
> a few comments below.
>
> On Wed, Jan 12, 2011 at 7:41 AM, Dudo <dudomail_at_gmail.com> wrote:
> > Hi,
> > I met the same problems with visualization of VTF trajectories as some
> folks
> > some time ago (seek in the thread).
> > I don't know how those guys solved the problem, or how they do visualize
> > their trajectories.
> > The thing is, that the VTF pluggin in VMD is most likely malfunctional.
> It
> > doesn't work with the default inputs from
> > their webpage.
>
> rather than complaining in this very unspecific way,
> can you provide examples or pointers to examples
> that "don't work" and then explain what does not
> work how, and what you would have expected instead.
> this way, somebody else has a chance to reproduce
> the situation and come up with suggestions.
> when you refer to a thread on the mailing list, please
> provide an URL.
> also, it is of vital importance to know which version
> of VMD you are using and on what platform.
> in general, the easier it is for somebody else to
> reproduce your problem, the easier you will be helped.
>
> furthermore, have you considered contacting the author
> of the VTF plugin, olaf lenz, about the problems. he would
> certainly be _most_ interested to know of problems with
> it and try to resolve them.
>
> [...]
>
> > at this point VMD looks to me however as more straightforward tool, where
> > you can get your visualization in the fastest way.
> > So, it appeared to me as a simplest possibility to convert from VTF to
> other
> > format, particularly LAMMPSTRJ.
> > For those, who find this a convenient option, I'm providing the source
> code
> > in the attachment.
> > If you compute trajectories on a cluster and then download the trajectory
> to
> > visualize how the structure evolves,
> > as I do, you can convert the trajectory on that machine.
> > Hence, in Linux you compile the code:
> > ifort vtf2lammps.f90
> > next, rename compilation output file
> > cp a.out vtf2lammps
> > make it executable
>
> how complicated!
>
> ever head of using the -o flag of the compiler?
> or using "mv" to rename files?
>
> > chmod +x vt*
> > You may run it by typing
> > ./vtf2lammps
> > then the program asks for an input file name. It changes its extension to
> > .lammpstrj so you don't provide a name for an output file.
> > you may use it also directly as a command with argument
> > ./vtf2lammps [filename]
>
> > in the VMD the grains will appear as tiny dots, I don't know why. It
> works
>
> that usually happens, when VMD has insufficient information
> about the system and thus cannot make any guesses to
> assign elements and bonds. the LAMMPS trajectory file
> by default contains limited information.
>
> > like this also for the default inputs from the pluggin website.
> > hence, you just click on the VMD main window, Graphics tab, from the top
> > menu, Representations,
> > choose CPK and increase the size of the spheres as you wish.
>
> a better way would be to provide a "topology" file that assigns
> elements and bonds, or running some tcl scripting that will assign
> atom radii, names, masses and more.
>
> > anyways, for a quick look you don't have to do that. it's sufficient to
> see,
> > that polymer is a polymer and e.g. doesn't fall apart.
>
> > one more thing, i was not sure about meaning of required inputs for PBC
> > BOUNDS in the lammps format.
>
> this is discussed in the lammps documentation of the dump command. RTFM!
>
> axel.
>
> > so if you have to correct it, it can be easily done in the source file,
> and
> > then please let me know too :-))
> > bye,
> > Dudo Racko
> > --
> > ____________________
> > Ing. Dusan Racko, PhD
> > Polymer Institute of the Slovak Academy of Sciences
> > Dubravska cesta 3
> > 845 41 Bratislava, Slovak Republic
> > tel: +421 2 5477 3448
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
-- ____________________ Ing. Dusan Racko, PhD Polymer Institute of the Slovak Academy of Sciences Dubravska cesta 3 845 41 Bratislava, Slovak Republic tel: +421 2 5477 3448
- Next message: John Stone: "Re: problem in extracting frame number"
- Previous message: Ali, Rejwan: "RE: Issues with Paratools and Gaussian"
- In reply to: Axel Kohlmeyer: "Re: VTF trajectory from coarse grained ESPReSo simulations. Visualization in Windows."
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]