137. Setting up Gaussian g09 on debian -- precompiled binaries

Most people would use a precompiled and pre-installed copy of gaussian on their local computational grid. If you do, however, purchase your own copy, or work at an institution with a site license, then you can install gaussian on your local beowulf cluster (or over-powered desktop).

And it's easy. I've presumed that your username is verahill, and your group is verahill.

You need csh

sudo apt-get install csh

Next set up a destination directory

mkdir /opt/gaussian
sudo chown verahill:verahill /opt/gaussian

copy the gaussian binaries to /opt/gaussian/g09 so that you have

/opt/gaussian/g09
|-- basis
|-- bsd
`-- tests
    |-- com
    |-- ia64
    `-- newz

Gaussian wants almost everything to be executable
chmod +x /opt/gaussian/g09/*
chmod +x /opt/gaussian/g09/bsd/*
cd /opt/gaussian/g09
csh bsd/install

Next, edit your ~/.bashrc and add (anywhere)

export g09root=/opt/gaussian
export GAUSS_SCRDIR=/scratch
. /opt/gaussian/g09/bsd/g09.profile
export PATH=$PATH:/opt/gaussian/g09/bsd:/opt/gaussian/g09/local

Source your bashrc to make changes take effect immediately:

source ~/.bashrc

You need to edit the bashrc of anyone wanting to use gaussian

And you're done!

136. Compiling GIMP 2.8 on Debian Wheezy/Testing

EDIT 14/12/2012: To use an ugly approach to running gimp 2.8 on debian stable/squeeze, look here:
http://verahill.blogspot.com.au/2012/12/running-gimp-28-in-chroot-on-debian.html
It ain't pretty...

EDIT 27/05/2012: GIMP 2.8 is now in the debian testing repos.

GIMP 2.8 is out -- and it's got the fabled single-window mode: http://www.phoronix.com/scan.php?page=news_item&px=MTA5NjA

First you need to install babl >=0.1.10, and gegl-0.2 >= 0.2.0,  then you can compile and install GIMP 2.8. The versions of babel and gegl in the debian testing/wheezy repos are too old, so you will need to compile tboth babel and gegl yourself -- luckily it is very easy to do so (see below).

Building with python script support needed a ton of packages (it requires PyGTK which depends on pygobject which depends on glib and gobject-introspection etc.), so here I passed --disable-python during build. It just means you can't script gimp with python. No python.

As always, I only spot what packages are missing on my system. If you find that other packages are missing, let me know in the comment section and I'll expand the post. At a minimum, you will need build-essential

LMDE MINT USERS: it seems like you need to add a single line to your /etc/ld.so.conf file:

/usr/local/lib

Then do
sudo ldconfig 

ldconfig is in the package libc-bin

Both babl and gegl are gimp specific, so not giving install prefixes is probably ok. Just don't try to uninstall the pre-existing versions or gnome will disappear on you. See here http://forums.linuxmint.com/viewtopic.php?f=190&t=101253 for more LMDE discussions. See here http://cloudplasma.co.uk/2012/05/gimp-2-8-on-linux-mint-debian-edition/ for a compile based on this post.

START HERE
0. sudo apt-get install build-essential libatk1.0-dev libfontconfig1-dev libcairo2-dev libgudev-1.0-0 libdbus-1-dev libdbus-glib-1-dev liblcms1-dev libexif-dev libxfixes-dev libgtk2.0-dev python2.7-dev libtiff4-dev libpango1.0-dev

1. babl 0.1.10
wget ftp://ftp.gtk.org/pub/babl/0.1/babl-0.1.10.tar.bz2
tar xvf babl-0.1.10.tar.bz2
cd babl-0.1.10/
./configure
make
sudo make install

2. gegl 0.2.0
sudo apt-get install libglib2.0-dev zlib1g-dev
wget ftp://ftp.gtk.org/pub/gegl/0.2/gegl-0.2.0.tar.bz2
tar xvf gegl-0.2.0.tar.bz2 
cd gegl-0.2.0/
./configure
make
sudo make install

3. gimp 2.8.0
sudo apt-get install intltool
wget ftp://ftp.gimp.org/pub/gimp/v2.8/gimp-2.8.0.tar.bz2
tar xvf gimp-2.8.0.tar.bz2 
cd gimp-2.8.0/
./configure --prefix=/home/me/.gimp --disable-python
make
make install

3. ~/.bashrc

Chuck the following in your ~/.bashrc

alias gimp28='/home/me/.gimp/bin/gimp-2.8'

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib

and source it. (source ~/.bashrc)

Start from the terminal using

gimp28

Done!

You can turn on single-window mode, by going to Windows and checking Single-Window Mode.

Edit: posted the how-to above eight hours ago, and already linked to by Debian-facile :-)

---

Links to this post:
http://forums.linuxmint.com/viewtopic.php?t=101253&f=190
http://cloudplasma.co.uk/2012/05/gimp-2-8-on-linux-mint-debian-edition/
http://linuxmint-fr.org/forum/graphisme/92501-installation-de-gimp-28.html

135. Oniom in gaussian -- with a little bit of help from gromacs and openbabel

Example -- I want to do explicit solvent modelling of methanol in water. This is obviously an articifical approach, but generally applicable.

This is a rough approach to doing oniom calculations using gaussian 09

1. Pre-optimisation
Draw methanol and set up a simple calc using e.g. ecce to pre-optimise the structure with e.g. an implicit solvent model. Here's g03.g03in:

  1 %nprocshared=4
  2 %Chk=g09_oniom.chk
  3 #P rb3lyp/GEN 5D Opt=()  Freq=()  Punch=(MO) Pop=() scrf=(pcm,solvent=water)
  4 
  5 g09_oniom
  6 
  7 0 1 ! charge and multiplicity
  8  C     0.00000     0.00000     0.00000
  9  H     -0.675500     -0.675500     0.675500
 10  H     0.675500     -0.675500     -0.675500
 11  H     -0.675500     0.675500     -0.675500
 12  O     0.866025     0.866025     0.866025
 13  H     1.51843     0.213620     1.51843
 14 
 15  H  0
 16  S   3  1.00
 17       18.73113700      0.03349500
 18        2.82539400      0.23472700
 19        0.64012200      0.81375700
 20  S   1  1.00
 21        0.16127800      1.00000000
 22  ****
 23  O  0
 24  S   6  1.00
 25     5484.67170000      0.00183100
 26      825.23495000      0.01395000
 27      188.04696000      0.06844500
 28       52.96450000      0.23271400
 29       16.89757000      0.47019300
 30        5.79963500      0.35852100
 31  SP  3  1.00
 32       15.53961600     -0.11077800      0.07087400
 33        3.59993400     -0.14802600      0.33975300
 34        1.01376200      1.13076700      0.72715900
 35  SP  1  1.00
 36        0.27000600      1.00000000      1.00000000
 37  SP  1  1.00
 38        0.08450000      1.00000000      1.00000000
 39  D   1  1.00
 40        0.80000000      1.00000000
 41  ****
 42  C  0
 43  S   6  1.00
 44     3047.52490000      0.00183500
 45      457.36951000      0.01403700
 46      103.94869000      0.06884300
 47       29.21015500      0.23218400
 48        9.28666300      0.46794100
 49        3.16392700      0.36231200
 50  SP  3  1.00
 51        7.86827200     -0.11933200      0.06899900
 52        1.88128800     -0.16085400      0.31642400
 53        0.54424900      1.14345600      0.74430800
 54  SP  1  1.00
 55        0.16871400      1.00000000      1.00000000
 56  SP  1  1.00
 57        0.04380000      1.00000000      1.00000000
 58  D   1  1.00
 59        0.80000000      1.00000000
 60  ****

2. Solvation using gromacs

Take the output, g03.g03out, and use babel to export the optimised structure

babel -ig09 g03.g03out -oxyz molecule.xyz

The next few steps require gromacs:

editconf -f molecule.xyz -o molecule.gro -box 2 2 2

genbox -cp molecule.gro -cs spc216.gro -o solvated.gro

babel -igro solvated.gro -oxyz solvated.xyz

Because I'm lazy, I then add an extra column for high/low, chop off the first few lines, and add a column with zeros...because that works. Not sure what that's actually for. Molecule?

tail -n +3 solvated.xyz | gawk '{print $1,"0",$2,$3,$4,"Low"}'>oniom.xyz

Edit oniom.xyz by hand and change the lines with "Low" to "High" (or just H) for the atoms in the methanol molecule.

C 0 10.14000 10.34000 10.00000 High
H 0 9.65000 10.75000 10.90000 High
H 0 9.65000 10.75000 9.10000 High
H 0 11.19000 10.65000 10.00000 High
O 0 10.14000 8.91000 10.00000 High
H 0 9.22000 8.60000 10.00000 High
O 0 5.69000 12.75000 11.65000 Low
H 0 4.76000 12.68000 11.28000 Low
H 0 5.80000 13.64000 12.09000 Low
O 0 15.55000 15.11000 7.03000 Low
[..]

cp oniom.xyz oniom.in

Edit oniom.in and put in your gaussian instructions, e.g.:

%chk=methanol_explicit.chk
%mem=500MB
%nprocshared=3
#Oniom(rb3lyp/6-31+g*:uff) maxdisk=6000MB opt=()

Methanol in explicit water

0 1 0 1 0 1
C 0 10.14000 10.34000 10.00000 High
[...]

So, you specify Oniom(high level:low level) -- here dft and MM (via uff -- amber and charmm are available too -- but then you must carefully define the atom types. See here).

You don't always, but sometimes, have to specify the spin/multiplicity of the high and low level systems as well as the total spin and multiplicity. Anyway, you can: First the overall, the the high, then the low level. E.g. we have a chromium compound with an unpaired spin of 1 (multiplicity=2) and a charge of +3, and have a MM shell with five sodium atoms and a multiplicity of 1 (spin=0). The total charge is 8 and total multiplicity is 2. The line would read 8 2 3 2 0 1.

That's it! You're ready to roll.

The run takes about 3 minutes.

That's it!