Re: Concatenate Outputs

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Sat Nov 10 2018 - 14:52:45 CST

  I am going to try and answer my own post here for those who will need this in the future. To concatenate all of the ORCA output files, use qmSecProc in your NAMD config under the QM part of the file. Place a file with this code:

#!/bin/bash

if [ ${1} ! -f mergedOrca.out ]; then
    echo "" > QMMM-Min.out.orc
fi

#echo "Input: qmmm_0.input"
cat ${1}.TmpOut >> QMMM-Min.out.orc

in the file where your qmBaseDir path is specified in your NAMD config QM part of the file. Make sure all of the files in that path, including the file with aforementioned code, has permission to be accessed.

  Now, I think I found a bug with concatenating the .TmpOut files from an ORCA job. At least, it seems the VMD orcaplugin has trouble if you specify more than one qmConfigLine in your NAMD config QM part of the file. Example:

  Concatenating your output files each step works with this format:

     qmConfigLine "! UKS B3LYP def2-TZVP ENGRAD Grid5 NoFinalGrid StrongSCF slowConv printbasis"
     qmConfigLine "%%output PrintLevel Mini Print\[ P_Mulliken \] 1 Print\[P_AtCharges_M\] 1 end"
     qmConfigLine "%%output Print\[ P_Basis \] 2 Print\[ P_MOs \] 1 end"

  i.e. only one qmConfigLine input line

  Concatenating your ORCA output files causes problems for the VMD orcaplugin if you use something like this:

qmConfigLine ! UKS B3LYP def2-TZVP
 qmConfigLine ! ENGRAD Grid5 NoFinalGrid StrongSCF slowConv printbasis
qmConfigLine "%%output PrintLevel Mini Print\[ P_Mulliken \] 1 Print\[P_AtCharges_M\] 1 end"
qmConfigLine "%%output Print\[ P_Basis \] 2 Print\[ P_MOs \] 1 end"

i.e. more than one input line. This may be obvious to everyone else. I learned the hard way. I

Kelly L. McGuire

PhD Scholar

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: Friday, November 9, 2018 1:12:21 PM
To: namd-l_at_ks.uiuc.edu; VMD Mailing LIst
Subject: namd-l: Concatenate Outputs

How do I concatenate or save the orbitals every step to a file that can be opened in VMD for viewing orbitals using the ORCA file type? I ran a QM/MM with ORCA.

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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