Re: AMBER: set a trucated octahedron box in Leap

From: Vlad Cojocaru <Vlad.Cojocaru.eml-r.villa-bosch.de>
Date: Tue, 12 Sep 2006 10:30:06 +0200

Thanks David for the answer,

Of course I did that but the problem is that I need also a top file
which contains the periodicity info ... Without box info in the top
file, periodic MD wont run ... So, I will set the IFBOX to 2 and then
copy the %FLAG BOX DIM from the initial top file ... Is there anything
else I should consider?

Best wishes
vlad



David A. Case wrote:

>On Mon, Sep 11, 2006, Vlad Cojocaru wrote:
>
>
>>I have an equilibrated periodic system (truncated octahedron box) and I
>>want to do a very small modification of the system using Leap. In the
>>meantime I want to retain all info regarding periodicity (box shape and
>>dimensions).
>>
>>
>
>For truncated octahedron, you probably will have to manually edit the last
>line of the coordinate file to match what was there in the earlier file
>(before the change).
>
>...good luck...dac
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
>

-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru.eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Sep 13 2006 - 06:07:12 PDT
Custom Search