RE: Angle of lone pair in TIP4P 2005 simulation

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue May 08 2018 - 19:57:31 CDT

Did you ever call "regenerate angles dihedrals" in building your psf? Or used something else that automatically generates angles if two atoms share a neighboring atom? NAMD is clearly telling you that you've built an angle there one way or another when you prepared the psf. The obvious solution, if you are positively sure that there shouldn't be an angle term there, is to just add a angle into your parameter set with a zero force constant. A better solution would be to figure out where in your psf construction process these angles are being introduced, and eliminate them.

-Josh

On 2018-05-08 18:21:47-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

Hi George,
You described the situation very well!
Best,
Esmael

On May 8, 2018, at 7:08 PM, Geo Reuter <georeuter_at_gmail.com<mailto:georeuter_at_gmail.com>> wrote:

Hello,
I am trying to do a minimization of a TIP4P 2005 waterbox and got this error:
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT OT LP (ATOMS 3 1 2)
This confuses me because from my understanding there should be no angle for the lone pair in the TIP4P 2005 water model. The topology file I used contains no angle so I thought this was the case. Does anyone have experience using TIP4P 2005 and could tell me what went wrong in my minimization.

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