From windemut { *at * } cumbnd.bioc.columbia.edu Tue Feb 28 13:38:02 1995 Received: from cumbnd.bioc.columbia.edu for windemut' at \`cumbnd.bioc.columbia.edu by www.ccl.net (8.6.9/930601.1506) id NAA02543; Tue, 28 Feb 1995 13:38:00 -0500 Received: from sirius by cumbnd.bioc.columbia.edu (NX5.67d/NX3.0M) id AA24600; Tue, 28 Feb 95 13:37:53 -0500 From: Andreas Windemuth Message-Id: <9502281837.AA24600 -x- at -x- cumbnd.bioc.columbia.edu> Received: by sirius.bioc.columbia.edu (NX5.67d/NX3.0X) id AA25968; Tue, 28 Feb 95 13:37:54 -0500 Date: Tue, 28 Feb 95 13:37:54 -0500 Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: chemistry %! at !% ccl.net Subject: Parallel Molecular Dynamics with full Coulomb interactions Cc: windemut-: at :-cumbnd.bioc.columbia.edu Status: R For those interested in parallel and scalable molecular dynamics simulation of biological macromolecules: Version 0.9 of the program PMD has been made available. This is an experimental program that uses the Greengard/ Rokhlin fast multipole algorithm (FMA) in conjunction with a constant force multiple timestep method to permit the efficient simulation of large biological macromolecules without cutting off the long range forces. For more details, see "http://tincan.bioc.columbia.edu/pmd/" or the README file from the distribution reproduced below. --- Andreas Windemuth +-------------------------------------------------------------------- |Columbia University, Department of Biochemistry and Biophysics |630 West 168th St. BB-221 | tel: (212)-305-6884, fax: 6926, NeXTmail |New York, NY 10032 | email: windemut-: at :-cumbnd.bioc.columbia.edu +-------------------------------------------------------------------- This is an experimental version of PMD, Version 0.9, release Feb 28, 1995, all rights reserved. PMD is a scalable, parallel program for the simulation of the dynamics of biological macromolecules. PMD utilizes the Greengard/Rokhlin Fast Multipole Algorithm to allow the simulation of very large biological macromolecular systems without sacrificing the important long-range Coulomb interactions. The force field implemented by PMD is compatible to programs such as CHARMM, X-PLOR, GROMOS, Discover and others. Residue topology and parameter files suitable for X-PLOR can be used with PMD. Particularly, PMD can fully implement the CHARMM19 CHARMM22 force fields. PMD is also intrinsically and transparently parallel and suitable for running on a wide variety of parallel architectures, both shared memory and message passing. The most salient features of PMD are: - Use of the Fast Multipole Algorithm allows for the calculation of the full long range electrostatic interactions in linear (of order N) time. - The Distance Class Algorithm reduces the calculation time further to make full-range calculations faster than conventional cutoff methods. - PMD is designed to be completely scalable, i.e. arbitrarily large systems (millions of atoms) can be simulated as long as enough processing nodes are available. Memory use is minimal, compared to other programs. - PMD runs without changes on a large number of UNIX workstations and can easily be adapted to others. Parallel implementations exist for the CM-5, the Intel Paragon, the Cray T3D and workstation networks. - Parallel instructions are limited to a small set of commands that are easily implemented in any machine specific or portable (TCGMSG, PVM, Linda) parallel processing interface. PMD is work in progress. Expect plenty of changes of all kinds in future versions. This program is made available to encourage researchers to add features they need and in the hope that some of these improvements find their way back into future versions. A mailing list has been established to foster discussion among users and contributors. Please direct inquiries to join the mailing list to "pmd-request # - at - # cumbnd.bioc.columbia.edu". The source code is being made available under the condition that any additions, improvements or changes will be sent to the author (windemut-0at0-cumbnd.bioc.columbia.edu) for inclusion into the distribution. No restrictions different from those on PMD itself may be put on such contributions. PMD or parts of it may not be used or distributed for non-disclosed corporate research or commercially without prior consent of the author. If either the program or ideas from its code are used in a publication, it is asked that the following references be cited: J.A. Board Jr., J.W. Causey, J.F. Leathrum Jr., A. Windemuth, and K. Schulten. Accelerated molecular dynamics simulation with the parallel fast multipole algorithm. Chem. Phys. Lett. 198:89--94, 1992. A. Windemuth and K. Schulten. Molecular dynamics on the Connection Machine. Molecular Simulation, 5:353--361, 1991. A. Windemuth. Advanced Algorithms for Molecular Dynamics Simulation: The Program PMD. in "Parallel Computing in Computational Chemistry" (Timothy G. Mattson, ed.), ACS Books, 1995, in press. Installation: cd zcat pmd.tar.Z | tar xvf - Demo run: cd pmd/demo make SYS= (one of next hpux dec iris aix sun paragon) Parallel demo run: [install TCGMSG and customize bin/par.] cd demo make SYS= PSYS=tcgmsg This will start a simulation of Pancreatic Trypsin Inhibitor (PTI), starting from the original PDB file, adding hydrogens, equilibrating with harmonic constraints and a minimizing. Look at "demo/makefile" and "src/make.sim" to see how the run is controlled and how you might modify it to run your own molecules. First, try changing the line "SYS=next" to reflect the machine you are actually using. Then, try "make MOL=mb" to run the solvated myoglobin setup that is frequently used as a benchmark for CHARMM. Finally, try "make mutant" to generate a Ile 3 -> Tyr mutant of T4 phage lysozyme (2lzm). Some of these simulation will take quite some time if not interrupted. It is suggested to run them in the background using the ampersand ("&") character, i.e. "make mutant &". The link "demo/log" will always point to the newest simulation log. Try "tail -f log" to check on the simulation progress. Some other sample molecules are available in "demo". Their topology is described in files "*.str", their atom coordinates in files "*.pdb". It is quite straightforward to make your own "*.str" files, once you study the sample files and "src/make.sim". If you wish to run PMD in parallel, make sure that you have TCGMSG or PVM installed and that there is a directory or link "tcgmsg" or "pvm" in your home directory pointing to your system's TCGMSG or PVM root directory. Edit "makefile" and change the line "PSYS=serial" to one of the supported parallel interfaces (tcgmsg, pvm, pvm-t3d). You also will have to edit a startup script that sets up processes on the network. The script has the name "par-$(SYS)-$(PSYS)" and it is located in "bin". Some examples are provided, but you will almost certainly have to adapt one of them to your own environment. TCGMSG can be obtained from "ftp.tcg.anl.gov". See the file "README.TCGMSG" for more information. Information on PVM can be obtained at "http://www.epm.ornl.gov/pvm/pvm_home.html" on the World-Wide Web. For information on the Cray T3D refer to "http://pscinfo.psc.edu/machines/cray/t3d/t3d.html". Documentation: This file, some scattered comments in makefiles and scripts, and the World Wide Web pages. Main features: Fast multipole algorithm Linear scaling enables simulation of extremely large systems Full long range interactions with no cut-off Distance class algorithm Accounts for full long-range interaction while providing performance better than conventional cut-off calculations Scalable parallel implementation on Workstation networks (with TCGMSG or PVM) Cray T3D (PVM) Convex Exemplar (TCGMSG) Intel Paragon (TCGMSG) Thinking Machines CM-5 (slow, no vector units, no longer supported) Parsytec GC (initial implementation, no longer supported) Now implemented: Growing of hydrogens Mutation (Growing of sidechains) Building solvation shells Superposition and RMS-values Solvent accessible surface (no forces, yet) Harmonic constraints Stochastic boundary (friction and random fluctuations) Restart files and DCD trajectories Main limitations: FMA and atom reassignment not fully scalable (yet) No vectorization Not enough features Forthcoming: (no guarantees, of course :-) ) Advanced solvent treatment Generalized Born potential Hydrophobic forces and continuum electrostatics with forces FMA and atom reassignment Improved scalable versions Periodic boundary conditions Other features Containment fields for closed boundary Pretty pictures (ray-tracing and movies) Adapting PMD to other parallel systems: All machine-specific parallel communication commands have been isolated into one file, called the adaptor. The adaptors in the current release are "tcgmsg.c": for the TCGMSG public domain parallel programming Interface, "pvm.c": for the PVM public domain parallel programming Interface, "cm5.c": for the Connection Machine 5 with CMMD-3.0, "pvm-t3d.c" for the restricted set of PVM used on the Cray T3D, and "serial.c": for non-parallel workstation implementations. With TCGMSG or PVM PMD can be run on a wide variety of platforms, such as workstation networks, the Intel Paragon and the Convex Exemplar. Other adaptors are expected to become available as work progresses. Changes from 0.8: - Much improved makefiles and compilation - Simplified parallel execution - Parallel output is now much faster and should always work - new trajectory format, with PDB and DCD conversion utility - PVM and the Cray T3D are now supported - Numerous bugs corrected. - Everything else also improved. Have fun! Andreas Windemuth +-------------------------------------------------------------------- |Columbia University, Dept. of Biochemistry and Biophysics, BB-221 |630 West 168th St. | tel: (212)-305-6884, fax: 6926, NeXTmail |New York, NY 10032 | email: windemut;at;cumbne.bioc.columbia.edu +--------------------------------------------------------------------