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Re: [ESPResSo-users] example object-in-fluid.tcl

From: Axel Arnold
Subject: Re: [ESPResSo-users] example object-in-fluid.tcl
Date: Fri, 31 Jan 2014 17:12:47 +0100
User-agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:24.0) Gecko/20100101 Thunderbird/24.2.0


vsf is only the structure information, and does not contain positions. The vtf format actually specifies three file types:

vsf - structure only
vcf - coordinates only
vtf - both together

If the file is called simEspresso.vsf, I would not expect coordinates in it, there should be some separate .vcf file. However, if an IMD connection to VMD is to be used, a .vsf file would be written to setup up the topology, and then VMD would need to connect to Espresso to get the coordinates, using its imd command.


On 31.01.14 10:39, Markus Gusenbauer wrote:
Hi Marco,

is it a problem of ESPResSo or VMD? Where exactly does the problem occur? Can you post the output!


PS: Don't forget to add address@hidden to the adresses!

On 30.01.2014 16:26, Marco Dallavalle wrote:
Dear Dr. Gusenbauer,

thank you for your quick reply. The version I'm using should be the latest, Espresso 3.2.0.

I was indeed missing a key in the myconfig.h file. Still it's not possible to visualize the result. The simEspresso.vsf file that has been generated seems incomplete with respect to the standard vtf format -> After the bonds are defined, no coordinates are printed.

Sincerely, Marco Dallavalle.

P.s. I subscribed to the mailing list.
From: Markus Gusenbauer address@hidden
Sent: Monday, January 27, 2014 11:26 AM
To: Marco Dallavalle; address@hidden
Subject: Re: example object-in-fluid.tcl

Hi Marco,

please subscribe to the official mailing list
( Maybe
someone else can use the information or can reply to your question.

Which version of ESPResSo do you use? For object-in-fluid.tcl you need


in myconfig.h.

Best wishes,

On 01/23/2014 05:09 PM, Marco Dallavalle wrote:
Dear Dr. Gusenbauer,

as a new user of the ESPResSo software I got interested in your object-in-fluid implementation.

I started going through the example object-in-fluid.tcl provided in the samples directory. Unfortunately some error occurs and the simulation gets stuck at the "add_oif_object" instruction. (I did not changed the tcl file, nor the input directory. The last lines it prints is "generating global area force bonds".) Could it be, that I'm not using the proper features in the myconfig.h file?

Thank you in advance for any help you might be able to provide.

Sincerely, Marco Dallavalle.

PhD student - Università di Bologna

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

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