Cerius2
by Accelrys, Inc.
Cerius
2 is a user-friendly graphical
molecular modelling program developed by Accelrys Inc. (formerly MSI) that incorporates a wide variety of popular molecular modelling codes in
materials sciences, life sciences and drug design. The Laboratory for Molecular Simulation, in collaboration with faculty in the departments of
Chemistry, Biochemistry & Biophysics, Chemical Engineering, and Environmental Engineering, has purchased licenses for a large number of the
modules available in cerius
2.
If you are a researcher at Texas A&M University and are interested in obtaining
access to this software, want to test a module that we currently do not have a license for, or simply have questions about the software, please contact
Lisa M. Pérez
Running Cerius2
The current version of Cerius
2 for SGI/IRIX machines is 4.10
To run cerius on your sgi machine you will need to add the following line to your .tcshrc file
alias cerius '/chem/cerius/cerius2/bin/cerius2'
To start the program from your SGI machine you will need to source your .tcshrc file to activate the new alias (source .tcshrc)
and then type: cerius at the prompt.
If you would like to run an
older version of Cerius
2 for SGI/IRIX, you will need to add additional aliases to your .tcshrc file:
alias cerius2vversion '/chem/cerius/cerius2_version/bin/cerius2'
where
version should be replaced with one of the available versions: 3.8, 4.8 or 4.9
For example, if you would like to run Cerius
2 4.9, you should create the following alias:
alias cerius2v4.9 '/chem/cerius/cerius2_4.9/bin/cerius2'
The current version of Cerius
2 for Linux is 4.11
To run cerius on your linux machine you will need to add the following line to your .tcshrc file
alias cerius '/chem/cerius/cerius2L/bin/cerius2'
note: The linux version of Cerius
2 does not contain all of the programs available in the IRIX version. Specifically, all of the quantum modules are missing
except the mopac module
For more information about Cerius
2 and the modules listed below, please visit:
Cerius2 Homepage or
Cerius2 Documentation.
The Cerius
2 documentation link will ask for a username and password. Please e-mail a request for the username and password to
Lisa M. Pérez
Modules Available For Use Through The LMS
| Module name | Number of Licenses |
| ADF (Amsterdam Density Functional)* | 1 |
| Amorphous Builder | 1 |
| Cation Locator | 2 |
| CASTEP | 1 |
| CFF Force Field | 12 |
| Confomers | 1 |
| Crystal Builder | 3 |
| Descriptor+ | 1 |
| Diffraction-Amorphous | 1 |
| Diffraction-Crystal | 2 |
| Diffraction-Faulted | 2 |
| DLS (Distance Least Squares) | 1 |
| DMol3 | 4 |
| DSolid | 1 |
| DMol3 Interface | 1 |
| Dynamics | 18 |
| ESOCS | 1 |
| Fast Structure | 1 |
| Force Field Editor (FFE) | 2 |
| Genetic Algorithms | 1 |
| Guassian Interface | 8 |
| HRTEM | 1 |
| Interface Builder | 2 |
| IR/RAMAN | 1 |
| LEED/RHEED | 1 |
| Mechanical Properties | 1 |
| Minimizer | 18 |
| MOPAC | 16 |
| Open Force Field | 22 |
| Powder Indexing | 1 |
| Polymer Builder | 1 |
| QSAR+ | 1 |
| Rietveld (DBWS/GSAS) | 1 |
| SDK (Software Developer kit) | 1 |
| Sorption | 2 |
| Structure Predictor | 2 |
| Surface Builder | 1 |
| Visualizer | 20 |
| Zindo | 1 |
*Only works in Cerius2 3.8
Trouble-shooting:
If you receive the error: cerius - command not found
type:
source .tcshrc at the prompt and try again. If you still receive a command not found error, you need to check the alias in
your .tcshrc file to make sure that it is properly defined. If your alias is correct then you should check to see if the /chem directory
has been mounted on your machine by typing
df at the prompt.
If /chem is not listed in the column under 'Mounted on', it is not mounted on your machine you will need to mount it before you can run the cerius program.
If /chem has been mounted on your machine in the past you will need to login as root and type:
/sbin/mount -h chmsgi
if this does not mount /chem (type df to determine if /chem is mounted) check to make sure that you have the following line in your /etc/fstab file:
chmsgi.chem.tamu.edu:/chem /chem nfs soft,intr,bg 0 0
If this line is in your fstab file and you still cannot mount /chem on your machine, contact your system administrator.
If you are running on a remote machine and you receive the error:
Xlib: connection to "labmol4.chem.tamu.edu:0.0" refused by server
Xlib: Client is not authorized to connect to Server
Error: Can't open display:labmol4.chem.tamu.edu:0.0
(where labmol4 will be replaced by the local machine name)
You need to make sure that you use the -X flag when you ssh to the remote machine (
ssh -X username@remote_machine_name )
If you are accessing the remote machine from a Linux box, you will probably need to use both the -X and -Y flags when you ssh to the remote machine.
