Re: rigidBonds water option

From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Feb 02 2012 - 14:02:37 CST

Assuming you aren't interested in sub-picosecond dynamics of water-hydrogen
sigma bonds or those of intermolecular hydrogen bonds to water ... yes,
rigid waters is fine. HOWEVER, TIP3P parameters were actually developed
with rigid bonds, so take this into account.

Best,
Chris

On Thu, Feb 2, 2012 at 1:48 AM, Hasan haska <hasanhaska_at_yahoo.com> wrote:

> Dear NAMD users,
>
> I want to perform md simulations with the namd.conf file ( in attached )
> in NVT ensamble for an interface system. The system includes water and one
> type of molecule . Also I want to use “rigidBonds water” option for
> equilibration and production run. Does this cause any problems with the simulations
> when I do trajectory analysis ? Can I get consistent results with
> experimental datas when I use “rigidBonds water” option ?
>
> Kind regards.
>

-- 
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 773-570-6078
http://www.ks.uiuc.edu/~char                Fax: 217-244-6078

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