Re: vmd-l: Re: Truncated Octahedron for VMD and NAMD simulation

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Fri May 16 2008 - 09:51:44 CDT

Hi,

Well, its a matter of what force field you want to use. If you want to
use the CHARMM force field, you cannot use the AMBER software (the LEAP
program, more precisely) to prepare your system. But if you want to use
the AMBER forcefield and for some good reason you want to do your
simulations with NAMD and not with sander or pmemd (from the AMBER
suite), it is possible to prepare your system in LEAP and run the
simulations in NAMD (see the NAMD manual which has very good
explanations of how to use the AMBER force field in NAMD).

I didn't know that VMD can solvate in truncated octahedron box.

Vlad

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
> <mailto: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://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

-- 
----------------------------------------------------------------------------
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/
----------------------------------------------------------------------------
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
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