VMD-L Mailing List

From: Bishop, Thomas C (bishop_at_tulane.edu)
Date: Fri May 16 2008 - 13:39:16 CDT

Just FYI the truncated oct. for dummies tutorial provided by TECIII
is at

http://amber.ch.ic.ac.uk/archive/200404/0038.html

This is code used in sander (or at least it was in 2004)

Tom

On Fri, 2008-05-16 at 10:42 -0400, Yinglong Miao wrote:
> Hi, Vlad-
>
> Thanks for your reply!
>
> I intended to use VMD to prepare the system outputting PSF and PDB
> files for NAMD simulation. But if I use AMBER, can the output files be
> used as input for NAMD simulation?
>
> Thanks,
> Yinglong
>
> On Fri, May 16, 2008 at 4:29 AM, Vlad Cojocaru
> <Vlad.Cojocaru_at_eml-r.villa-bosch.de> wrote:
> Which program do you intend to use to create you truncated
> octahedron ? If its AMBER, please note that the vectors
> described by Gromacs won't work.
> If you do use AMBER to create your box, please check the AMBER
> mailing list archives ... this issue has been discussed there
>
> Best
> vlad
>
> George Madalin Giambasu wrote:
> 1) Check out the Gromacs manual for how to specify the
> vectors of the unit cell for the truncated oct.
> 2) Make an estimate on how big the length of an edge
> of the oct. would be, enter the values of the cell
> vectors in an Namd configuration file and let your
> system equilibrate with NPT for a 1-2ns. Specify
> "wrapnearest on" and, in the end, you will get
> truncated oct. shaped sytem.
>
> I hope this helps,
>
> George
>
>
>
>
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> EML Research gGmbH
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
>
> Tel: ++49-6221-533266
> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
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>
>
>
>
>
> --
> Yinglong Miao
> Ph.D. Candidate
> Center for Cell and Virus Theory
> Chemistry Department, Indiana University
> 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
> Tel: 1-812-856-0981 

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