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Re: [ESPResSo-users] Coloring in VMD


From: Axel Arnold
Subject: Re: [ESPResSo-users] Coloring in VMD
Date: Sat, 24 May 2014 10:37:50 +0200
User-agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:24.0) Gecko/20100101 Thunderbird/24.5.0

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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