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Re: [ESPResSo-users] Coloring in VMD

From: Olaf Lenz
Subject: Re: [ESPResSo-users] Coloring in VMD
Date: Sun, 25 May 2014 12:27:17 +0200

You can either use off-line visualization by using the commands "writevsf" and "writevcf" into a VTF file and then visualize it using "vmd <filename>.vtf":

  # these lines replace the "prepare_vmd_connection"
  set file [open "sim.vtf" "w"]
  writevsf ignore_charges $file

  # this replaces "imd positions"
  writevcf $file
  # and at the end
  close $file

For online visualization, you can use just what you did in your first mailing if you have no charged atoms:

  prepare_vmd_connection aaa 3000
  exec sleep 4
  imd positions

...however, to be able to distinguish the atoms, do not use the Coloring Method "segname", but "type" instead. 
If you do have charged atoms, you either have to use the current development code, or you have to modify the code of "prepare_vmd_connection" in scripts/auxiliary.tcl".


2014-05-25 11:58 GMT+02:00 Narges Nikoofard <address@hidden>:
Dear Dr. Arnold,

Many thanks for the answer.

I see in userguide that "ignore_charges" is used with "writevsf" command. Does it mean that I should write vtf files and then use VMD for visualizing them? Or, this is still possible to use "prepare_vmd_connection" for automatically setting up a VMD connection?

If the latter is possible, much less effort is needed.

Thanks again,
Narges Nikoofard

On Sat, May 24, 2014 at 1:07 PM, Axel Arnold <address@hidden> wrote:
Dear Narges,

Espresso 3.2.0 uses vtf rather than PDB for communication with VMD. Therefore, SegName is no longer used, but just Type or Name. Type just gives the type number from Espresso.

However, the vtf plugin in VMD has a bug, which cannot handle charges correctly and wipes the type and name information. So, if your systems are charged, you either need to switch to the latest development release, or use the workaround option "ignore_charges" to prepare_vmd_connection.

Best regards,

On 24.05.14 08:18, Narges Nikoofard wrote:
Dear all,

I have two types (0 and 1) of particles in my system. I use these lines to visualize my system in VMD:

prepare_vmd_connection aaa 3000
exec sleep 4
imd positions

Unfortunately, the two types of particles are colored the same in VMD. I use version 3.2.0 of ESPResSo.
I have checked Graphics --> Representations --> Coloring Method: SegName

I would be grateful, if someone could kindly help me.

Many thanks in advance,
Narges Nikoofard

JP Dr. Axel Arnold
ICP, Universität Stuttgart
Allmandring 3
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609

Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607

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