Re: vmd-l: Bugs and Questions

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

Ah I see ok. And what about having a +2 ion in the QM region, do I need to include other atoms that make the region +/- 1, or leave the region a total of +2?

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Joao Ribeiro <jribeiro_at_ks.uiuc.edu>
Sent: Thursday, April 25, 2019 1:22 PM
To: McGuire, Kelly; namd-l_at_ks.uiuc.edu; VMD Mailing LIst
Subject: Re: vmd-l: Bugs and Questions

There you go.

QwikMD is currently not able to use psf/pdb pair as a starting point, if this files are not loaded during the QwikMD input file loading process. The QM/MM (https://www.ks.uiuc.edu/Research/qmmm/Tutorial/Tutorial.pdf) tutorial actually demonstrate how you can prepare a QM/MM simulation from a MM simulation prepared by QwikMD.

Best

Joao

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

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

jribeiro_at_illinois.edu<mailto: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 2:16 PM
To: Joao Ribeiro <jribeiro_at_ks.uiuc.edu>, "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, VMD Mailing LIst <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Bugs and Questions

I save the last frame of my MM equilibration as a PDB, and then use that in QwikMD to make my QMMM files.

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________

From: Joao Ribeiro <jribeiro_at_ks.uiuc.edu>
Sent: Thursday, April 25, 2019 1:14 PM
To: McGuire, Kelly; namd-l_at_ks.uiuc.edu; VMD Mailing LIst
Subject: Re: vmd-l: Bugs and Questions

Are you preparing the QM simulation from a previous MM simulation that prepared in QwikMD, or from just a pdb file? If it is from a pdb file, that information is not contained in the file, the reason why the charges are not updated.

Best

Joao

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

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

jribeiro_at_illinois.edu<mailto:jribeiro_at_illinois.edu>

+1 (217) 3005851

From: "McGuire, Kelly" <mcg05004_at_byui.edu>
Date: Thursday, April 25, 2019 at 2:10 PM
To: Joao Ribeiro <jribeiro_at_ks.uiuc.edu>, "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, VMD Mailing LIst <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Bugs and Questions

Ok, the solvent selection works by pressing return. The charge of my QM region is still a problem though in 1.9.4a31 with QwikMD beta. Doesn't update until after the files are written. The charge needs to be +/- 1, correct? I have a copper atom in the QM region, which is a +2 charge. Do I still need to make the region +/- even when there are ions in the QM region?

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________

From: Joao Ribeiro <jribeiro_at_ks.uiuc.edu>
Sent: Thursday, April 25, 2019 12:39 PM
To: McGuire, Kelly; namd-l_at_ks.uiuc.edu; VMD Mailing LIst
Subject: Re: vmd-l: Bugs and Questions

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<mailto: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

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:20:45 CST