External Software Issues

Solutions for ORCA, GROMACS, and Multiwfn configuration and execution problems

Table of Contents

• Overview
• ORCA Issues
• GROMACS Issues
• Multiwfn Issues
• Common Path Issues
• License and Installation
• See Also

Overview

External software issues typically fall into these categories:

Software	Common Issues	Environment Variables
ORCA	Path, MPI, license	OHMind_ORCA, OHMind_MPI
GROMACS	PATH, GPU, topology	MD_WORK_DIR
Multiwfn	Path, input files	MULTIWFN_PATH, MULTIWFN_WORK_DIR

ORCA Issues

ORCA Binary Not Found

Symptom:

FileNotFoundError: ORCA executable not found

Solutions:

1. Set ORCA path:

   export OHMind_ORCA="/path/to/orca/orca"
   

2. Verify path is correct:

   ls -la "$OHMind_ORCA"
   # Should show the orca executable
   

3. Add to .env:

   OHMind_ORCA=/opt/orca/orca
   

4. Test ORCA:

   "$OHMind_ORCA" --version
   

MPI Configuration Issues

Symptom:

Error: MPI not found or misconfigured

Solutions:

1. Set MPI path:

   export OHMind_MPI="/usr/lib/openmpi/bin"
   

2. Verify MPI installation:

   ls -la "$OHMind_MPI/mpirun"
   "$OHMind_MPI/mpirun" --version
   

3. Check ORCA-MPI compatibility:
   • ORCA requires specific OpenMPI versions
   • Check ORCA documentation for compatible versions
4. Add MPI to PATH:

   export PATH="$OHMind_MPI:$PATH"
   export LD_LIBRARY_PATH="/usr/lib/openmpi/lib:$LD_LIBRARY_PATH"
   

ORCA Calculation Fails

Symptom:

ORCA finished with error code 1

Solutions:

1. Check ORCA output file:

   cat "$QM_WORK_DIR/job_name.out" | tail -50
   

2. Common errors and fixes:

   Memory error:

   # In ORCA input, increase memory
   %maxcore 4000  # 4GB per core
   

   Convergence failure:

   # Try different SCF settings
   %scf
     MaxIter 500
     DIISMaxEq 15
   end
   

   Basis set not found:

   # Check ORCA basis set library path
   ls "$ORCA_PATH/../share/orca/basis"
   

3. Check disk space:

   df -h "$QM_WORK_DIR"
   

QM_WORK_DIR Issues

Symptom:

PermissionError: Cannot write to QM_WORK_DIR

Solutions:

1. Create and set permissions:

   mkdir -p "$QM_WORK_DIR"
   chmod 755 "$QM_WORK_DIR"
   

2. Check disk space:

   df -h "$QM_WORK_DIR"
   # ORCA can generate large temporary files
   

3. Clean old files:

   # Remove old temporary directories
   find "$QM_WORK_DIR" -name "temp_*" -mtime +7 -exec rm -rf {} \;
   

ORCA License Issues

Symptom:

ORCA requires a valid license

Solutions:

1. Register at ORCA forum:
   • Visit: https://orcaforum.kofo.mpg.de/
   • Register for academic license
2. Download correct version:
   • Match your system architecture
   • Use version compatible with your MPI

GROMACS Issues

GROMACS Not in PATH

Symptom:

gmx: command not found

Solutions:

1. Source GROMACS environment:

   source /path/to/gromacs/bin/GMXRC
   

2. Add to PATH manually:

   export PATH="/path/to/gromacs/bin:$PATH"
   

3. Verify installation:

   which gmx
   gmx --version
   

4. Add to .bashrc for persistence:

   echo 'source /path/to/gromacs/bin/GMXRC' >> ~/.bashrc
   

GPU/CUDA Issues

Symptom:

GROMACS was compiled without GPU support

Solutions:

1. Check GROMACS GPU support:

   gmx mdrun -version | grep GPU
   

2. Install GPU-enabled GROMACS:

   # Build with CUDA support
   cmake .. -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
   make -j$(nproc)
   make install
   

3. Check CUDA availability:

   nvidia-smi
   nvcc --version
   

Topology Errors

Symptom:

Fatal error: No such moleculetype XXX

Solutions:

1. Check force field files:

   ls /path/to/gromacs/share/gromacs/top/
   

2. Verify topology includes:

   ; In topology file
   #include "amber99sb.ff/forcefield.itp"
   

3. Check molecule definitions:

   grep "moleculetype" topology.top
   

MD_WORK_DIR Issues

Symptom:

Cannot create output files in MD_WORK_DIR

Solutions:

1. Create directory:

   mkdir -p "$MD_WORK_DIR"
   chmod 755 "$MD_WORK_DIR"
   

2. Check disk space:

   df -h "$MD_WORK_DIR"
   # MD trajectories can be very large
   

3. Clean old simulations:

   # Remove old trajectory files
   find "$MD_WORK_DIR" -name "*.xtc" -mtime +30 -exec rm {} \;
   

Simulation Crashes

Symptom:

Fatal error: Step XXX: The domain decomposition grid has shifted too much

Solutions:

1. Check system setup:
   • Verify box size is appropriate
   • Check for overlapping atoms
2. Reduce time step:

   ; In mdp file
   dt = 0.001  ; 1 fs instead of 2 fs
   

3. Improve energy minimization:

   gmx mdrun -v -deffnm em -nsteps 50000
   

4. Check for bad contacts:

   gmx grompp -f em.mdp -c system.gro -p topol.top -o em.tpr -maxwarn 1
   

Multiwfn Issues

Multiwfn Binary Not Found

Symptom:

FileNotFoundError: Multiwfn executable not found

Solutions:

1. Set Multiwfn path:

   export MULTIWFN_PATH="/path/to/Multiwfn/Multiwfn"
   

2. Verify path:

   ls -la "$MULTIWFN_PATH"
   "$MULTIWFN_PATH" << EOF
   q
   EOF
   

3. Add to .env:

   MULTIWFN_PATH=/opt/Multiwfn/Multiwfn
   

Missing Input Files

Symptom:

Error: Cannot find wavefunction file

Solutions:

1. Check file exists:

   ls -la "$MULTIWFN_WORK_DIR"/*.wfn
   ls -la "$MULTIWFN_WORK_DIR"/*.molden
   

2. Generate wavefunction from ORCA:

   # In ORCA input
   %output
     Print[P_MOs] 1
     Print[P_Basis] 2
   end
   

3. Convert formats if needed:

   # Multiwfn can read: .wfn, .wfx, .molden, .fch, .gbw
   

MULTIWFN_WORK_DIR Issues

Symptom:

Cannot write output to MULTIWFN_WORK_DIR

Solutions:

1. Create directory:

   mkdir -p "$MULTIWFN_WORK_DIR"
   chmod 755 "$MULTIWFN_WORK_DIR"
   

2. Check permissions:

   touch "$MULTIWFN_WORK_DIR/test" && rm "$MULTIWFN_WORK_DIR/test"
   

Multiwfn Analysis Fails

Symptom:

Error in Multiwfn analysis

Solutions:

1. Check Multiwfn output:

   cat "$MULTIWFN_WORK_DIR/analysis.log"
   

2. Run interactively to debug:

   cd "$MULTIWFN_WORK_DIR"
   "$MULTIWFN_PATH" input.wfn
   # Follow prompts manually
   

3. Check input file format:
   • Ensure wavefunction file is complete
   • Verify file is not corrupted

Display/GUI Issues

Symptom:

Error: Cannot open display

Solutions:

1. Run in text mode:

   # Multiwfn can run without GUI
   export DISPLAY=""
   

2. Use X forwarding:

   ssh -X user@server
   

3. Install required libraries:

   # For GUI support
   sudo apt-get install libgtk-3-0 libglu1-mesa
   

Common Path Issues

Environment Variables Not Set

Symptom: Various “not found” errors

Solutions:

1. Check all required variables:

   echo "OHMind_ORCA: $OHMind_ORCA"
   echo "OHMind_MPI: $OHMind_MPI"
   echo "MULTIWFN_PATH: $MULTIWFN_PATH"
   echo "QM_WORK_DIR: $QM_WORK_DIR"
   echo "MD_WORK_DIR: $MD_WORK_DIR"
   echo "MULTIWFN_WORK_DIR: $MULTIWFN_WORK_DIR"
   

2. Set in .env file:

   # External software paths
   OHMind_ORCA=/opt/orca/orca
   OHMind_MPI=/usr/lib/openmpi/bin
   MULTIWFN_PATH=/opt/Multiwfn/Multiwfn
      
   # Work directories
   QM_WORK_DIR=${OHMind_workspace}/QM
   MD_WORK_DIR=${OHMind_workspace}/MD
   MULTIWFN_WORK_DIR=${OHMind_workspace}/Multiwfn
   

3. Source in startup script:

   # In start_OHMind.sh
   source .env
   

Library Path Issues

Symptom:

error while loading shared libraries: libXXX.so

Solutions:

1. Add to LD_LIBRARY_PATH:

   export LD_LIBRARY_PATH="/path/to/libs:$LD_LIBRARY_PATH"
   

2. Install missing libraries:

   # Find which package provides the library
   apt-file search libXXX.so
   sudo apt-get install package-name
   

3. Use ldconfig:

   sudo ldconfig
   

License and Installation

ORCA Installation

1. Register at ORCA forum:
   • https://orcaforum.kofo.mpg.de/
2. Download and extract:

   tar -xf orca_5_0_4_linux_x86-64_shared_openmpi411.tar.xz
   mv orca_5_0_4_linux_x86-64_shared_openmpi411 /opt/orca
   

3. Set environment:

   export OHMind_ORCA=/opt/orca/orca
   export PATH="/opt/orca:$PATH"
   export LD_LIBRARY_PATH="/opt/orca:$LD_LIBRARY_PATH"
   

GROMACS Installation

1. Install via package manager:

   sudo apt-get install gromacs
   

2. Or build from source:

   wget https://ftp.gromacs.org/gromacs/gromacs-2023.tar.gz
   tar -xf gromacs-2023.tar.gz
   cd gromacs-2023
   mkdir build && cd build
   cmake .. -DGMX_BUILD_OWN_FFTW=ON
   make -j$(nproc)
   sudo make install
   source /usr/local/gromacs/bin/GMXRC
   

Multiwfn Installation

1. Download from:
   • http://sobereva.com/multiwfn/
2. Extract and set up:

   unzip Multiwfn_3.8_bin_Linux.zip
   mv Multiwfn_3.8_bin_Linux /opt/Multiwfn
   chmod +x /opt/Multiwfn/Multiwfn
   export MULTIWFN_PATH=/opt/Multiwfn/Multiwfn
   

Diagnostic Script

#!/bin/bash
# external_software_check.sh

echo "=== External Software Check ==="

# ORCA
echo ""
echo "1. ORCA:"
if [ -n "$OHMind_ORCA" ] && [ -x "$OHMind_ORCA" ]; then
    echo "   ✅ Path: $OHMind_ORCA"
    version=$("$OHMind_ORCA" --version 2>&1 | head -1)
    echo "   Version: $version"
else
    echo "   ❌ Not configured or not executable"
    echo "   OHMind_ORCA=$OHMind_ORCA"
fi

# MPI
echo ""
echo "2. MPI:"
if [ -n "$OHMind_MPI" ] && [ -x "$OHMind_MPI/mpirun" ]; then
    echo "   ✅ Path: $OHMind_MPI"
    version=$("$OHMind_MPI/mpirun" --version 2>&1 | head -1)
    echo "   Version: $version"
else
    echo "   ❌ Not configured or not executable"
    echo "   OHMind_MPI=$OHMind_MPI"
fi

# GROMACS
echo ""
echo "3. GROMACS:"
if command -v gmx &> /dev/null; then
    echo "   ✅ Path: $(which gmx)"
    version=$(gmx --version 2>&1 | grep "GROMACS version" | head -1)
    echo "   $version"
else
    echo "   ❌ Not found in PATH"
fi

# Multiwfn
echo ""
echo "4. Multiwfn:"
if [ -n "$MULTIWFN_PATH" ] && [ -x "$MULTIWFN_PATH" ]; then
    echo "   ✅ Path: $MULTIWFN_PATH"
else
    echo "   ❌ Not configured or not executable"
    echo "   MULTIWFN_PATH=$MULTIWFN_PATH"
fi

# Work directories
echo ""
echo "5. Work Directories:"
for dir in QM_WORK_DIR MD_WORK_DIR MULTIWFN_WORK_DIR; do
    path="${!dir}"
    if [ -d "$path" ] && [ -w "$path" ]; then
        echo "   ✅ $dir: $path"
    else
        echo "   ❌ $dir: $path (missing or not writable)"
    fi
done

echo ""
echo "=== Check Complete ==="

See Also

• Troubleshooting Overview - Main troubleshooting guide
• Installation Issues - Setup problems
• MCP Issues - Server connection problems
• Configuration Reference - Environment setup
• ORCA Server - ORCA MCP documentation
• GROMACS Server - GROMACS MCP documentation
• Multiwfn Server - Multiwfn MCP documentation

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*Last updated: 2025-12-23

OHMind v0.1.0*