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.
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'
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?
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
The minimization and constant T simulation input files are attached.
The rigid bond option did not work when used in Minimization simulation.
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