Angstrom symbol XMGrace

How do I get the Angstrom symbol to show up in labels, titles, text?
ISO Latin encodings were added to the PostScript driver by Przemek Klosowski (przemek@rrdbartok.nist.gov).
You can now print the Angstrom symbol.
There is no onscreen display of the extended characters (something will show, but it won't be right).
3.02 will use the xvertext routines so that it will be a bit more WYSIWYG.
Use \c to go into the upper 128 characters and \C to return to normal.
\cE\C is the Angstrom symbol.

Angstrom Symbol in XMgrace

How do I get the Angstrom symbol to show up in labels, titles, text?

ISO Latin encodings were added to the PostScript driver by Przemek
Klosowski (przemek@rrdbartok.nist.gov).
You can now print the Angstrom
symbol. There is no onscreen display of the extended characters (something
will show, but it won't be right).
3.02 will use the xvertext routines
so that it will be a bit more WYSIWYG.
Use \c to go into the upper
128 characters and \C to return to normal.
\cE\C is the Angstrom symbol routines
so that it will be a bit more WYSIWYG.

GAUSSIAN 03 KeyWords

#P
Additional output is generated. This includes messages at the beginning and end of each link giving assorted machine-dependent information (including execution timing data), as well as covergence information in the SCF.

RHF
This method keyword requests a Hartree-Fock calculation. Unless explicitly specified, RHF is used for singlets and UHF for higher multiplicities. In the latter case, separate α and β orbitals will be computed [57,58,59]. RHF, ROHF or UHF can also be specified explicitly. SCF single point energy calculations involving basis sets which include diffuse functions should use the SCF=Tight keyword to request tight SCF convergence criteria.

MaxDisk
The MaxDisk keyword specifies the amount of disk storage available for scratch data, in 8-byte words. The value may optionally be followed by a units designation: KB, MB, GB, KW, MW or GB. Normally, this is set for a site in the site-wide Default.Route file.

MP2 calc. PickT4: no shell combinations can fit!

This ERROR typically indicates memory problems. Increase the amount of memory
requested with the %mem keyword.

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"
****************************************************

Procedure to create Hidrocarbon DL_POLY/GULP Input Force Field

1. Create file fort.8 from a template.car file, with columns 62-63 modified according to the codes (See con2fie.f):

• c it distinguishes : c1,c2,c3 as sp3 carbons: primary, sec., tert.
• c it distinguishes : ca = C(sp2), c6 = C(arom), n4 =N(cuaternary)
• c it distinguishes : h = H , o = O
• c it distinguishes : c9 = C(carbonyl, as in C=O)
• c it assigns : c0 = general c1,c2,c3
• c it assigns : c4 = C(cuaternary)
• c (otherwise you can relabel 'c4' to 'c3' if pots are the same)
• c it assigns : n0 = general n1,n2,n3

2. Create a connectivity file fort.9 from a .pdb file template.pdb . The template.pdb file is obtained from the template.car file using babel:

babel -icar template.car -opdb template.pdb
awk -f pdb2con.awk < template.pdb > fort.9

3. The files fort.11, fort.12 and fort.13 are fixed and they must be in the directory.

4. Run the con2fie executable, which is going to generate the fort.1, fort.10 and fort.14 files. These files are the the input files for DL_POLY (fort.1, fort.10 ) and GULP (fort.14).
./con2fie

5. Run the awk scripts skip-repeated.awk onto fort.14

awk -f skip_repeated.awk < fort.14 > fort.14-1

and

awk -f forcefield_repeated.awk < fort.14-1> fort.14-2

6. If a torsion term makes part of the force field, then add a number code following the rule:
n=3 if Angle= 0.0
n=2 if Angle= 180.0

example:
torsion bond intra
h core c1 core ca core h core 0.0108 0.0
h core ca core ca core h core 0.3254 180.0
Add:
torsion bond intra
h core c1 core ca core h core 0.0108 3 0.0
h core ca core ca core h core 0.3254 2 180.0

7. You're ready to go. The file fort.14-2 is your Hydrocarbon ForceField in GULP format.

8. Files fort.1 and fort.10 are the files needed by DL_POLY FIELD file. fort.1 has information about the 2-Body, 3-Body and Dihedral intramolecular force field. fort.10 is a check-out file with 2, 3 and 4 body connectivity.

9. Charges for the forcefield are obtained from the template.car using the "charges.awk" awk script.

awk -f charges.awk < template.car > template.charges

The output file contains the individual charges of every atom in the molecule and the average charge value for atom type.