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Re: [ESPResSo-users] Coloring in VMD


From: Narges Nikoofard
Subject: Re: [ESPResSo-users] Coloring in VMD
Date: Sun, 25 May 2014 14:28:26 +0430

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,
Axel


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, Universit├Ąt Stuttgart
Allmandring 3
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609



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