qmSecProc Proper Use

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Fri Nov 02 2018 - 15:02:00 CDT

   I am trying to use the grab_orca.sh file from the QM/MM O2 example. I add qmSecProc grab_orca.sh to my config file, but the job crashes if I do that. How do I properly use qmSecProc to save the orbital information from ORCA every step? If I run grab_orca.sh after the job is done and in the same directory as the .TmpOut file, then I get the it works, but trying to do this every step with qmSecProc causes problems. Doing this would allow me to open the .orc file in VMD and see the orbitals for every frame. Here is the grab_orca.sh file:

#!/bin/bash

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

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

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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