Re: problem with water molecules angle in MD simulation

From: Tristan Croll (
Date: Fri Jan 30 2015 - 02:43:42 CST

That's a question for someone who knows the guts of NAMD a lot better than I. For the time being, if you're worried about it a simple workaround would be to write an extrabonds file to maintain either the angle or the H-H distance during minimization. Try this in the tkconsole:

set outfile [open extrabonds-water.txt w]

set bondstrength 200

set Hdist 1.598

set water [atomselect top water]

foreach res [lsort -unique [$water get residue]] {

  set thisH1 [atomselect top "residue $res and name H1"]

  set thisH2 [atomselect top "residue $res and name H2"]

  set H1index [$thisH1 get index]

  set H2index [$thisH2 get index]

  puts $outfile "bond $H1index $H2index $bondstrength $Hdist"


close $outfile

Then run your minimization with this extrabonds file applied, and remove it for the equilibrium dynamics.

From: Shoresh Shafei <>
Sent: Friday, 30 January 2015 6:28 PM
To: Tristan Croll
Cc:; Norman Geist
Subject: Re: namd-l: problem with water molecules angle in MD simulation


Thank you for tying it on your machine. The questions is why this is happening. Did you have any explanation for it?

Best Regards

On Jan 30, 2015, at 3:25 AM, Tristan Croll <<>> 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.


From:<> <<>> on behalf of Norman Geist <<>>
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?

Norman Geist.

Von: Shoresh Shafei []
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!

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