AW: problem with water molecules angle in MD simulation

From: Norman Geist (
Date: Tue Jan 27 2015 - 02:28:18 CST



actually I meant that you create a parm file with only one water molecule,
so I can compare it to my files.


You are right, the three bonds should fix the angle. You must also know that
the water models and so SHAKE (rigidbonds) are hard coded in NAMD. This
means if NAMD is somehow unable to detect your water as water, it won't
work. NAMD does this detection based on the atoms masses. This means you may
not change them.


The point about minimization might be correct, but I'm sure NAMD doesn't
turn of SHAKE during minimization.


Send me a parmfile with only one water. I've observed weird behavior earlier
when the leap.rc isn't properly set up.


Norman Geist.


Von: Shoresh Shafei []
Gesendet: Montag, 26. Januar 2015 17:54
An: Norman Geist
Betreff: Re: namd-l: problem with water molecules angle in MD simulation


Dear Norman,

Thank you for your prompt response.


As you mentioned, TIP3P does not have angle property, however, as far as I
remember two OH bonds are determined. Doesn't fixing "three bonds"
automatically fix the angle?


I was not sure what you meant by onewater.parm7 file so I directly replied
to your own email address.

All I could think of was parm10.dat that I use in Amber which is attached to
this email.


I really appreciate your help.





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