Re: alkane-silicon_dioxide simulation

From: Eduardo Cruz-Chu (chucruz_at_ks.uiuc.edu)
Date: Thu Jul 10 2008 - 15:46:25 CDT

On Thu, 10 Jul 2008, Raul Araya Secchi wrote:

>
> Dear NAMD Users:
>
> Im performing some simulations of an alcane box over a SiO2 waffer much like those reported by the people of NAMD with a water droplet,

Did you get the silica waffer from the Inorganic Builder plugin in VMD?.
That will provide you the right PSF/PDB structure. Otherwise, building the
right PSF is a real problem.

> I can run NPT simulations if I put the flexible cell on and useConstantArea on but the bottom of the SiO2 waffer appear in the top of the simulation box,

sure, NPT with constant area is the right thing (unless you are planing
to simulate an alcane drop, in which case you should use NVT). The upper
part of your cell is moving because the center of your cell is shifted. Just
relocate the center a little bit down.

>
>
>
>
> -- Raúl Araya Secchi
> B.Sc Molecular Biotechnology.
> Molecular Biotechnology Engineer.
> Centre for Bioinformatics CBUC,
> Faculty of Biological Sciences, P. Universidad Catolica de Chile
> Portugal # 49 – ZIP 6513492 Santiago – Chile Phone: + 56 2 6862269;
> http://www.cbuc.cl
>
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