Re: vmd-l: Bugs and Questions

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Thu Apr 25 2019 - 13:39:32 CDT

Hi Kelly,

 

Let me answer the QwikMD side of the “Bugs and Questions.”

 

Please update your VMD to the latest alpha release, as some issues were already fixed. There is also an updated version of QwikMD (QwikMD beta) that you can install. Please download QwikMD beta from http://www.ks.uiuc.edu/Research/qwikmd/.

 

I just tested the selections of water molecules, and the selection worked adequately. Please make sure that the number of atoms is updated correctly in the table and in the selection Window. It might be silly, but make sure that you press return in the distance entry, so the distance value is taken into account.

 

Give the new version a try and please let me know if it worked. If not, can you please a test case (privately if you must) so I can try?

 

The NAMD side I will have to leave for the experts.

 

Best

 

João

 

……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois

http://www.ks.uiuc.edu/~jribeiro/

jribeiro_at_illinois.edu

+1 (217) 3005851

 

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of "McGuire, Kelly" <mcg05004_at_byui.edu>
Date: Thursday, April 25, 2019 at 10:14 AM
To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, VMD Mailing LIst <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Bugs and Questions

 

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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