Getting Started with Computational Chemistry at MCSR
Computational Chemistry Applications are available at MCSR?
- How can I submit
Gaussian jobs on sweetgum using PBS?
- How can I
submit Gaussian jobs on mimosa using PBS?
Where can I learn more about PBS on sweetgum?
- What does the error
"PBS: job killed: mem 142147584 exceeded limit 125829120" in my PBS error file
Why does the system not find the files that it needs (PBS script, user input
file, on /ptmp or home dir.)?
- How can I make the
read-write file span multiple physical files?
- Is there any way to
get the molecular orbitals in the same orientation as was used in the
Gaussian input file, rather than in Gaussian's standard
- How can I optimize the
geometry of thiophne at the MP2 level?
- Why did Gaussian
- What do these messages
(prefaced by >>>> below) from Gaussian mean?
Where can I learn more about Gaussian?
When I type g98sub to run Gaussian 98 on sweetgum, why do I get the message
not found or command not found?
- What is
NWChem, and how can I use it on sweetgum and mimosa?
- What is
GAMESS, and how can I use it on sweetgum and mimosa?
- What improvements does Gaussian 03 offer over Gaussian 98, and what do I have to do differently to run Gaussian 03 jobs on sweetgum?
What Computational Chemistry
Applications are available at MCSR?
Gaussian 94/98, GAMESS, NWCHEM on sweetgum
GAMESS on sweetgum and mimosa
Gaussian 03 on mimosa
Gaussian 03 on sweetgum
Gaussian 03 on redwood
NWCHEM on mimosa
NWCHEM on sweetgum
NWCHEM on redwood
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What does the error "PBS: job killed: mem 142147584
exceeded limit 125829120" in my PBS error file mean?
You must make sure you specify enough memory when you submit the job to PBS.
If in doubt, try
specifying a lot more memory than you think you need. You must also specify
enough memory in your
input file. Memory specified in the input file will take precedence over memory
specified to PBS.
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How can I make the read-write file span multiple
If I try something like this:
then the program just writes to the first file until it runs out of space on
If I give explicit sizes like this:
then I get an error message:
No file to extend for IUnit=1 --Out of disk space
Error termination in NtrErr
There is lots of disk space available on all of these disks, far more than 20
The value -1 says that a file segment may be enlarged without limit.
It is intended for use on the
final file segment only. Contrary to what is implied in the manual, -1
is not an option which means
use all available space and then go on to the next file. The information
required for this is not readily
available from most operating systems.
The value 0 says to retain the current size of an existing file
segment. Thus, it should not be used for file
segments which do not already exist. All other values are interpreted as
words, not as megawords. Thus,
your second example specified each file segment as 20 words in length, and that
fills up quickly. You need
to add the MW suffix to the value of 20 in your second example in order
for things to work properly.
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Is there any way to get the molecular orbitals in the
same orientation as was used in the Gaussian input file, rather than in
Gaussians standard orientation? (I want to be able to compare
the MOs in a series of related molecules, but the program doesn't give the
orbitals in a consistent orientation.)
You can use the NoSymm keyword to obtain this desired effect.
NoSymm tells Gaussian to ignore any
symmetry in the molecule, treating it as if it had no symmetry, and leaving the
molecule in the input orientation.
Using NoSymm will have significant performance consequences for
Hartree-Fock and DFT calculations,
and negligible to modest performance consequences for other calculation types.
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How can I optimize the geometry of thiophne at the MP2
(The job I ran exited without converging after 63 cycles, taking an enormous
amount of time on each point.
Whats wrong? Would I be better off using Cartesian coordinates?)
Route section from the job:
#P RMP2/3-21G** SCF=DIRECT FOPT MP2=STINGY
The problem is with your route. You have specified MP2 twice. This
results in an MP4 optimization, not one
at the MP2 level. As a result, you are using the FP optimizer, which only uses
energies and not gradients.
I would suggest that you use this route instead:
#P MP2/6-31G** SCF=Direct FOpt=CalcHFFC
for the following reasons:
MP2=Stingyonly affects MP2 frequency calculations, so you can leave that
(It is ignored in this case, so it wont actually hurt you either).
FOpt is a good idea; it does not change the optimization algorithm, but
adds a check to see that your
coordinates are really independent and span the space in which you are
However, an even better optimization method would be to compute the HF
frequencies at the first point
by using FOpt=CalcHFFC. The force constants are quite transferable
between basis sets and methods.
You should consider moving to 6-31G* or 631G** to really get the correlation as
opposed to basis set
incompleteness. In order to get systematic improvement with electron
correlation, you must use an
adequate basis set. The 3-21G** basis set suffers from considerable basis set
incompleteness, and 631G*
is the smallest basis set you should consider using.
The issue of Cartesian vs. internal coordinates is the subject of considerable
debate. In general, if you have
a good Z-matrix, an optimization with internals will be at least as fast as one
using Cartesian coordinates.
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I was running a large MP2 calculation when the job died
having filled my 1 GB scratch disk. I had used
MAXDISK=80000000 and MP2=DIRECT in the route section. Why did Gaussian
There are two common misunderstandings about MAXDISK: its units and
what it can control. The units are
REAL*8 words; divide the number of bytes you want by 8 to get the proper value
to specify to MAXDISK.
Since 80 million REAL*8 words is only 640 MB, you are correct that the scratch
disk usage should not exceed
the available disk space. The real problem is that the scratch space used for
the AO integrals is not included in
MAXDISK. In your case, you need to specify SCF=Direct to minimize
Certain calculation types also require fixed minimum amounts of scratch space
and thus cannot honor MAXDISK
when it is smaller. These include QCISD(T) and MP4SDTQ energies and QCISD
gradients. MP2 frequency
calculations also try to obey MAXDISK, but will consume more space if
that is the only way for execution to continue.
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What do these messages (prefaced by >>>> below) from
ONE-ELECTRON INTEGRALS COMPUTED USING PRISM. THE SMALLEST EIGENVALUE OF THE
OVERLAP MATRIX IS 1.527D-01 PROJECTED HUCKEL GUESS. REQUESTED CONVERGENCE ON RMS
DENSITY MATRIX=1.00D-08 WITHIN 64 CYCLES. REQUESTED CONVERGENCE ON MAX DENSITY
MATRIX=1.00D-06. INTEGRAL ACCURACY REDUCED TO 1.0D-05 UNTIL FINAL ITERATIONS.
>>>> PROBLEM DETECTED WITH INEXPENSIVE INTEGRALS. >>>> SWITCHING TO FULL
AND REPEATING LAST CYCLE.
Gaussian 98 attempts to perform the initial iterations of a
HartreeFock or Density Functional calculation using
aggressive cutoffs in order to speed up the calculation, then switching to more
accurate results as convergence is
approached. This message indicates that the cutoffs were found to be too
aggressive and the program switched
over to full accuracy early. There is no problem with the final converged
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what should I do if I get this error "/usr/local/apps/g98/linda-exe/l302.exel:
error while loading shared libraries: util.so: cannot open shared object file: No such file or directory"?
To run a g98 job on mimosa, you need to have a file called .cshrc in your
home/login directory, containing the following:
setenv g98root /usr/local/apps