From: Shoresh Shafei (s.shafei_at_gmail.com)
Date: Fri Jan 30 2015 - 02:28:17 CST
Tristan,
Thank you for tying it on your machine. The questions is why this is happening. Did you have any explanation for it?
Best Regards
Shoresh
> On Jan 30, 2015, at 3:25 AM, Tristan Croll <tristan.croll_at_qut.edu.au> wrote:
>
> I tried this out on my machine using TIP3P water, the CHARMM-36 forcefield, and NAMD 2.10, and I see the same thing. During energy minimization the water molecules adopt a wide range of angles down to about 95 degrees, but they all snap back to ideality as soon as the equilibrium simulation starts.
>
>
> Tristan
> From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Norman Geist <norman.geist_at_uni-greifswald.de>
> Sent: Thursday, 29 January 2015 5:56 PM
> To: 'Shoresh Shafei'
> Cc: namd-l_at_ks.uiuc.edu
> Subject: AW: namd-l: problem with water molecules angle in MD simulation
>
> Couldn’t see anything unsual. Have you already tried recreating the .top file, sometimes there are corruptions which lead to such behavior?
>
>
>
> Norman Geist.
>
>
>
> Von: Shoresh Shafei [mailto:s.shafei_at_gmail.com]
> Gesendet: Mittwoch, 28. Januar 2015 17:21
> An: Norman Geist
> Betreff: Re: namd-l: problem with water molecules angle in MD simulation
>
>
>
> Hi Norman,
>
> The minimization and constant T simulation input files are attached.
>
> The rigid bond option did not work when used in Minimization simulation.
>
> Thank You!
>
> Shoresh
>
>
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:36 CST