Bugs and Questions

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu Apr 25 2019 - 10:14:02 CDT

I have a few questions and possible bugs to report (VMD 1.9.4a12 and VMD 1.9.3a31):

1) In QwikMD, when I select my QM region, I put Solvent within QM region 3.5 (the value doesn't matter for this), and then click apply, those solvent molecules are not included in the qm-input.pdb file that QwikMD writes. Meaning, the beta column does not get filled with 1's for any of those solvent molecules included within that distance. I have to manually add the 1's to the beta column after QwikMD writes all of the files. Should the beta column be updated with 1's for those solvent molecules?

2) The charge of the QM region does not get updated until after QwikMD files are written. But, shouldn't the charge column show the charge of your selection so that we can make sure it is no greater than +/- 1?

3) Why does namd2 +p16 (or less) allow me to run QMMM with live solvent off, but namd2 +p20 (or higher) results in a crash with segmentation fault?

4) Sometimes I get the error:
ERROR: The number of QM atoms received (202) is different than expected: 205
FATAL ERROR: Problems broadcasting QM atoms.: No such file or directory

  Sometimes the QM atoms received is higher than the expected number too...

5) What are the reasons to use and not to use live solvent (LSS)? I understand that a MM water molecule is switched out with a QM water molecule every LSS freq seletion, but why is it necessary to switch those molecules? Diffusion of water molecules in the MM region into the QM region is unlikely on the time scales of QMMM, so I'm wondering what is the purpose of LSS?

Thanks!

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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