Running Gaussian in ITQCALC-machines

Before using Gaussian's newzmat tool set the memory stack to "unbound" by issuing the following command:

ulimit -s unlimited

RMSD from HISTORY file

How to calculate RMSD and Trajectories for adsorbates in zeolites from a DL_POLY HISTORY FILE:

1. Extract the Adsorbates from the HISTORY file using the his2hc.awk script.

awk -f his2hc.awk < HISTORY > HISTORY_hc

2. Create files fort.11 and fort.12 according to:
echo " 2 11 9999 0.1" > fort.11
where 2 is the number of molecules of adsorbate
11 is the number of atoms in each molecule
9999 is the number of steps in the simulation
0.1 is the timestep in picoseconds

echo "HISTORY_hc_com > fort.12
echo HISTORY_hc_com2 >> fort.12
echo 8 >> fort.12

where 8 is the number of guest molecules adsorbed.

3. Run the msd2.x fortran executable. Two files are generated HISTORY_hc_com and HISTORY_hc.msd.
HISTORY_hc_com contains the adsorbates center of mass coordinates in DL_POLY 2.x format.
HISTORY_hc.msd contains the rmsd data to be drawn using xmgrace

4. Create a file fort.12 with the name of the COM input and output files to be used to generate the two dimensional trajectories of the adsorbates. The last line of this file must contain the number of adsorbate molecules.
echo "HISTORY_hc_com" > fort.12
echo "HISTORY_hc_com2" >> fort.12
echo "2" >> fort.12

5. Transform the HISTORY_hc_com from PBC coordinates to corrected coordinates, HISTORY_hc_com2, using the binary file real_image2.x obtained from the corresponding fortran code real_image.f.

6. Finally, using the binary hc_traj.x calculate the two-dimensional trajectories of the adsorbates. The binary will ask the user for the following information:
Input hc file ?
HISTORY_hc_com2
Output file ?
SasPenPmm600
time interval between configurations (in ps) ?
0.05
number of monoatomic entities ?
8
and it will create 6 files:
trajx_SasPenPmm600
trajxy_SasPenPmm600
trajxz_SasPenPmm600
trajy_SasPenPmm600
trajyz_SasPenPmm600
trajz_SasPenPmm600
which can be draw using xmgrace.

Or in case of emergency use the following bash script (the information in fort.11 and fort.12 must be changed according to the situation) :
****************************************************************
#!/bin/bash

echo "Extracting HC from HISTORY"
awk -f his2hc.awk <> HISTORY_hc
echo "Done extracting HC from HISTORY"

echo "Creating fort.11 file"
rm -f fort.11
echo " 8 9 4950 0.10" > fort.11

echo "Calculating RMSD from HISTORY_hc file"
./msd2.x
echo "Done"

echo "Creating fort.12 file"
rm -f fort.12
echo "HISTORY_hc_com" > fort.12
echo "HISTORY_hc_com2" >> fort.12
echo "8" >> fort.12
echo "Done"

echo "Starting Real to Image"
./real_image2.x
echo "Done"

echo "Starting the Trajectories calculation"
echo "Be prepared to interact"
./hc_traj.x
echo "All set"
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