Re: Merge File Question

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Sun Apr 07 2019 - 00:47:23 CDT

I was able to concatenate the molden file for each step of my TeraChem/NAMD QMMM simulation. However, the VMDa12 Molden plugin only opens the first step/frame and none of the others. What needs to be done or what format does the file need to be in to get the Molden plugin to open multiple steps just like the ORCA plugin does for concatenated ORCA output files from QMMM?

Kelly L. McGuire

PhD Candidate

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, April 5, 2019 6:36 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Merge File Question

I have been using my trial version of TeraChem for benchmarking my QMMM simulations. I will have a benchmark report soon. I can already say that TeraChem with GPUs is significantly faster than ORCA for QMMM.

My question has to do with merging TeraChem orbital files just like with ORCA. I have this script that concatenates the .TmpOut files for ORCA and then I can open the orbitals for each frame of my QMMM trajectory. I can't get it to work with TeraChem's orbital files which have the .molden extension. Here is the code before I tried modification for TeraChem:

### File to merge the outputs of QM packages.
### Generated by QwikMD version 1.2.

#!/bin/bash

i="$IFS";IFS='/';set -f;p=($4);set +f;IFS="$i"
QMREGION=${p[-2]}
if [ ! -f ${1}.${QMREGION}.out ] && ((${5} != "0")) ; then
echo "" > ${1}.${QMREGION}.out
elif [ ! -f ${1}.${QMREGION}.out ] && ((${5} == "0" && ${3} != "-1")) ; then
cat ${4}.TmpOut > ${3}.${QMREGION}.out
fi
if ((${5} % ${2} == 0 && ${5} != "0")); then
cat ${4}.TmpOut >> ${1}.${QMREGION}.out
fi

In the qmmm_exec/QMMM/0/ directory that is created, TeraChem creates an additional directory:

qmmm_exec/QMMM/0/src/

The .molden file is stored there, it is called qmmm.molden. In the script above, what should I change to merge these files together so VMD can read them in just like it does for ORCA?

Kelly L. McGuire

PhD Candidate

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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