 | Required Literature Citations |
| Description |
| Supported Platforms |
| Distribution & Licensing |
| Documentation |
| Supporting OpenGL Remotely on a PC |
| Running MacroModel/Maestro/Batchmin at PUCC's SP/CC3 site |
Published work using BatchMin (the computational back-end of the MacroModel package) should cite:
Mohamadi, F., Richard, N. G. J., Guida, W. C., Liskamp R., Lipton, M., Caufield, C., Chang, G., Hendrickson, T., Still, W. C., "MacroModel - an Integrated Software System for Modeling Organic and Bioorganic Molecules Using Molecular Mechanics," J. Comput. Chem., (1990) 11, 440.
MacroModel is the generic term used to describe several programs which provide molecular visualization tools as well as semi-empirical molecular modeling calculations.
The term MacroModel may as well be used specifically for the front-end visualization of the complete MacroModel package. This front-end is being phased out in favor a new front-end called Maestro. This visualization package is based on X/OpenGL technology, so that X server programs supporting OpenGL can run on Unix, PC or Macintosh systems enabling the user to access the visualization tools remotely.
BatchMin is the batch-mode molecular modeling computation facility for use with MacroModel. It is designed to minimize the energy of one structure or a series of structures, to eliminate duplicate conformations, to do conformational searches and to conduct molecular dynamics simulations. BatchMin may be configured to run on the same system as the front-end visualization tool or remotely via several network protocols. Batchmin may also be run via a command line or via a batch queuing system.
| Intel/Linux (RedHat 5.2 or SUSE 6.2) |
| SGI/IRIX 6.5.2m |
| COMPAQ/Tru64 Unix V4.0F |
| HPUX 11.0 |
| IBM RS/6000/AIX 4.3.2.0. |
Maestro requires OpenGL extensions to the X server to run on all system except Intel/Linux. The MacroModel visualization program will run without OpenGL support (X-windows mode), but does not provide full functionality under that environment.
MacroModel, Maestro and Batchmin can be run from the SP/CC3 system at the Purdue University Computing Center.
Desktop access to a remote UNIX system running MacroModel (in particular, PUCC's SP/CC3 systems) is provided via X server software:
| Windows Platforms
| ||||
| UNIX workstations support an X-windows environment so that remote access to MacroModel from UNIX systems is also supported. 3D support for MacroModel front-end requires the use of IRIS GL, so that only SGI machines may utilize this functionality. OpenGL extensions are required for Maestro. |
The MacroModel suite of programs is licensed (i.e. a license file is required) on a per-subnet basis. Contact Jonathan Amy Facility for Chemical Instrumentation, Dept. of Chemistry for more information on licensing.
On-line documentation is available on Schrödinger, Inc.'s web site.
Documents in PDF format (readable with Adobe Acrobat Reader) are available as well. All Rights Reserved, Schrödinger, Inc.:
MacroModel Primer
MacroModel 7.0 User's Guide
MacroModel 7.0 Technical Guide
BatchMin 7.0 User's Guide
XCluster 7.0 User's Guide
MacroModel User Guide Update for
Version 7.1
MINTA Software Documentation
Support for OpenGL is made available through a volume license for Hummingbird's eXceed 3D module. Members of the Department of Chemistry can obtain this through from the office of the Jonathan Amy Facility for Chemical Instrumentation. Other parties should contact PACE for access to this software.
You must be sure to enable the GLX (OpenGL eXtension). To do this run Xconfig program, click Protocol; click Extensions...; click the GLX checkbox, also, if you do not have the SP/CC3 systems set up in the security file, you must click the checkbox in the insecure box as well.
Maestro is the preferred visual interface for remote visualization from the SP/CC3 site. To run Maestro from the SP/CC3 site, you should do the following:
| Apply for an account on the SP/CC3 using a Form 6 available in the
business office. (If you have an account on flash, lively, quick, or cloud, that is your SP/CC3 account). |
| If you are running from a PC, obtain a copy of Hummingbirds eXceed 3D from JAFCI, install and configure it on your workstation. Note that you do not need to install all (and in most instances should not install) the complete eXceed package, only the component's necessary for eXceed X-windows usage along with eXceed 3D module. Other workstations will require other software. SGI IRIX systems will have all the necessary software already installed. |
| Run eXceed (or whatever on your workstation's OpenGL-enable X server software is). |
| Log into cloud or another CC3 computer system using the eXceed connection tool or any other telnet program available to you. |
| Set the display environment variable. If your workstation's network (i.e. IP) name is xyz.chem.purdue.edu and you are using the csh command shell on cloud, the command is setenv DISPLAY xyz.chem.purdue.edu:0.0 |
| Set up the environment variable to the macromodel directory: setenv SCHRODINGER /usr/share/apps3/MacroModel7.1 |
| Execute the program with the command $SCHRODINGER/maestro |
Note that you may also use the interactive batch method outlined for MacroModel for Maestro as well to obtain a dedicated processor for a short time.
Batchmin may be run directly from the Maestro visual interface or may be run from the command line. See the Maestro/MacroModel documentation for a full explanation of this operation. The specifics for running Batchmin from Maestro on the SP/CC3 follow:
| There are two different job types for Batchmin: immediate and queued. |
| Immediate jobs are run on the same processor on which Maestro is running. When selecting Host for the job, select bmin-com. This can only be used for short/small jobs that will complete before you log out of the CC3 machine you use. This also allows for running jobs at the interactive batch level. |
| Queued jobs use the Portable Batch System (PBS) to run on a processor dedicated to your job. See the on-line documentation on the CC3/SP system for more information (command: man qsub). |
| Hosts beginning with rs_ or sp_ reflect the type of queue into which you desire to place the job. The queued job request will provide the maximum allowable time permitted for each queue (short: 30 minutes, large: 24 hours: huge: 6 days). |
| The hosts with -VER will immediately execute on specific hardware architectures utilizing hardware-specific features of Power2 and Power3 systems. Maestro/MacroModel must already be running on the proper architecture. |
| When using the queuing mechanism, Maestro (or MacroModel) will most often not detect the start of the job because of the time it takes to get the job running on a batch processor node. You can use the standard queue commands on the SP/CC3 systems to monitor the queue status of your job. Once the job is running you may use the Monitor... option of Maestro to monitor your BatchMin job. |
You may also directly queue a Batchmin job from the command line if you already have prepared a Batchmin job file (.com). The job file can be created from Maestro. This job file may be transferred from a separate system, but you must also remember to transfer the input file for the molecular structure (the .dat file) as well. A simple script, subbmin, has been written to submit a BatchMin job from the command line:
subbmin command-file-name queue-options
where command-file-name is the .com file's name without the .com extension and queue-options is a list with any of the options that the qsub will accept.
Because of a bug in the AIX implementation of the MacroModel visual interface, MacroModel MUST be run in interactive batch mode on the SP/CC3 systems. MacroModel also requires an X-windows interface for visualization. This may be eXceed or PC-Xware, both available for campus use. Once a interactive batch job has been established, running MacroModel is very similar to running Maestro.
| Apply for an account on the SP/CC3 using a Form 6 available in the
business office. (If you have an account on flash, lively, quick, or cloud, that is your SP/CC3 account). |
| If you are running from a PC, obtain a copy of Hummingbird's eXceed from JAFCI, install and configure it on your workstation. Note that you do not need to install all (and in most instances should not install) the complete eXceed package, only the component's necessary for eXceed X-windows usage. Other workstations will require other software. SGI IRIX systems will have all the necessary software already installed. |
| Run eXceed on your workstation (or whatever on your workstation's X server software is). |
| Log into cloud or another CC3 computer system using the eXceed connection tool or any other telnet program available to you. |
| Set the display environment variable. If your workstation's network (i.e. IP) name is xyz.chem.purdue.edu and you are using the csh command shell on cloud, the command is setenv DISPLAY xyz.chem.purdue.edu:0.0 |
| Set up the environment variable to the macromodel directory: setenv SCHRODINGER /usr/share/apps3/MacroModel7.1 |
| Execute the program with the command $SCHRODINGER/macromodel |
To enter interactive batch mode issue the following command:
qsub -I -q sp_short
The command will stall until a processor (dedicated to your job) becomes available, at which time a shell prompt running under that processor appears. Because the time allocated to interactive batch jobs are limited, you may only run for the period specified in the qsub command. See the online documentation for qsub on the SP/CC3 system (command: man qsub). If you wish to reserve more than one-half hour, you must specify a queue with longer wall-time or cpu-time maximums:
qsub -I -q sp_large -l walltime=00:45:00
reserves forty-five minutes for the interactive batch job. It may take a while to access an sp_large node; use sp_short to access one-half hour increments to reduce your wait time. Please exit interactive batch jobs shells when not in use so others may use the batch job nodes.
Note that each processor node of the SP system has its own IP address. You must configure your X server software to accept connections from the node that is allocated to you which is dynamically by the systems queuing mechanism.
