Re: Water Molecule Issue

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Wed Apr 24 2019 - 12:54:01 CDT

Update: This flickering appears when I select just the QM region atoms for my representation. If I show all atoms, QM and MM, then the water molecules aren't jumping. Also, if I do just show/represent the QM region atoms and turn on update selection every frame for the the waters representation, then the flickering also goes away. The water selection I have is waters within 6 angstroms of resname COP, which are all of the water molecules in the QM region and around the copper atom (resname COP). I do have live solvent turned on. Maybe the QM region water molecules are exchanging with the MM region water molecules...? Or maybe this is just a VMD drawing/representation phenomenon.

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: McGuire, Kelly
Sent: Wednesday, April 24, 2019 9:12 AM
To: namd-l_at_ks.uiuc.edu; McGuire, Kelly
Subject: Re: Water Molecule Issue

Also, on the final step, I get this error:

ERROR: The number of QM atoms received (208) is different than expected: 205
FATAL ERROR: Problems broadcasting QM atoms.: No such file or directory

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of McGuire, Kelly <mcg05004_at_byui.edu>
Sent: Wednesday, April 24, 2019 9:03 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Water Molecule Issue

I have a new QMMM system I am trying out. I have 4 imidazoles 6 angstroms away from a copper atom. They solvated in 40x40x40 water box. There are about 56 water molecules between the copper atom and the 4 imidazoles. I am including those waters, the 4 imidazoles, and the copper atom in my QM region. When I run my QMMM minimization step, the water molecules are acting strangely. For the first 50 steps, the appear to minimize correctly. But then every two steps afterward, i.e. step 51, 53, 55, etc....some of the QM water molecules (about 20 or so) jump or appear about 10-15 angstroms away from where they were. But in the other steps, i.e. 52, 54, 56, etc...they are back in there original positions. Why would the water molecules be moving so far in some of the minimization steps?

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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