From: Shoresh (s.shafei_at_gmail.com)
Date: Tue Jan 27 2015 - 10:30:54 CST
Hi Norman,
Thanks for all the useful hints you have provided.
The parameter file for one water molecule is attached.
Best,
Shoresh
On Tue, Jan 27, 2015 at 3:28 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:
> Hi,
>
>
>
> 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 [mailto:s.shafei_at_gmail.com]
> *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.
>
> Best
>
> Shoresh
>
>
>
>
>
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