alkane-silicon_dioxide simulation

From: Raul Araya Secchi (arayasecchi_at_hotmail.com)
Date: Thu Jul 10 2008 - 15:18:06 CDT

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, but Im having problems with the NPT simulation paramenters. Most of the time I got an error like this: PME Stray Carges ..... when I use NPT with the flexible cell off.
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, and I can tell why is that happening.
Please any help on how to do this kind of box over a big surface NPT simulations??? thanks.

-- 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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