From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Fri Jan 30 2015 - 02:25:32 CST
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
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