Last Update: Aug. 5 2004
PEACH ４.８ (Windows)
Release dates:
- PEACH 4.8 Aug. 5 2004
You can get PEACH Ver. 4.8(Windows) free of chargeif you follow the conditions below:
1.The user should not sell the original or modified programs of PEACH.
2.In publication of scietific data obtained by PEACH, state clearly the version of PEACH
and cite references.
3.Given that conditions (1) and (2) be followed,the user may modify or redistribute PEACH.
Please report to the author upon redistribution.
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** PEACH 4.8 with ABINIT-MP20021029 software license agreement **
The copyright holders of this software grant the license to use
the software if you accept the following terms of this agreement.
1. This software is provided without a fee and without any maintenance
service. The authors and copyright holders do not warrant any result this
software produces.
2. The licensee must not sell the source codes of this software,
either original or derivative. The licensee may redistribute the software,
both original and derivative, for free of charge, provided that they report
of the redistribution to the contact person in advance.
3. The licensee may sell the results obtained by use of this software
without permission.
4. Any reports or published results obtained by use of the software
should include acknowledgement of the software followed by the appropriate
citation of references as follows:
(A) When FMO and/or FMO-MD computations are performed,
Name of the software: PEACH 4.8 with ABINIT-MP20021029
Citation: references (1) and (2)
(B) When only other functions of the software are used,
Name of the software: PEACH 4.8
Citation: reference (3)
Also, appropriate references must be cited when force field (ff) parameters
are used: OPLS ff (reference 4), AMBER84 ff (5), AMBER86 ff (6),
AMBER94 ff (7), AMBER96 ff (7, 8), and AMBER99 ff (7,9).
REFERENCES
(1) Nakano, T., Kaminuma, T., Sato, T., Fukuzawa, K. Akiyama, Y.,
Uebayasi, M., Kitaura, K. (2002) Chem. Phys. Lett. 351, 475-480.
(2) Komeiji, Y., Nakano, T., Fukuzawa, K., Ueno, Y., Inadomi, Y.,
Nemoto, T., Uebayasi, M., Fedorov, D. G., Kitaura, K. (2003)
Chem. Phys. Lett., 372, 342-347.
(3) Komeiji, Y., Haraguchi, M., Nagashima, U. (2001) Parallel Computing 27,
977-987.
(4) Jorgensen, W. L., Tirado-Rives, J. (1988). J. Am. Chem. Soc. 110,
1657-1666.
(5) Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C.,
Alagona, G., Profeta, S., Weiner, P. (1984). J. Am. Chem. Soc. 106, 765-784.
(6) Weiner, S. J., Kollman, P .A., Nguyen, D. T., Case, D. A. (1986).
J. Comp. Chem. 7, 230-252.
(7) Cornell, W. D., Cieplak, P., Layly, C. I., Gould, I. R., Merz, K. M.,
Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., Kollman, P. A.
(1995). J. Am. Chem. Soc. 117, 5179-5197.
(8) Kollman, P. A., Dixon, R., Cornell, W., Fox, T., Chipot, C., Pohorille, A.
(1997) in Computer simulation of biomolecular systems
(Wilkinson, A., Weiner, P., Van Gunsteren, W., eds.), Vol. 3, pp. 83-96,
Kluwer/Escom.
(9) Wang, J., Cieplak, P., Kollman, P. A. (2000). J. Comput. Chem. 21,
1049-1074.
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[REGISTER] if you agree to follow the above conditions.
[DOWNLOAD] PEACH 4.8 if you have already registered.
[How to use] Japanese
化学ソフトウェア学会 ２００１年度大会 講演要旨（PDFファイル）
DESCRIPTION OF THE FILES CONTAINED IN PEACH_4.8
Windows Version by Yoshiro Nakata
Copy files from CD-ROM, and change the file properties.
you may find the directory tree below.
peach_4.8naka/
test/ same as original peach files
demo/ same as original peach files
doc/ same as original peach files
data/ same as original peach files
bench/ same as original peach files
special_data/ same as original peach files
src/ source files for visual fortran
EXE-W/ visual fortran workspace filse
RUN/ exe files for windows
PROT/ demo example on windows sysytem
PROT_DNA/ demo example on windows sysytem
GAS_PEPT/ demo example on windows sysytem
DNA_RNA/ demo example on windows sysytem
(A) TEST FILES (test/)
Four examples of MD and FMO-MD simulations are given here:
DNA and C16 peptide and AU and GAGAGA..
The files in this directory were constructed for short and simple tests of the
PEACH modules. They are not intended to serve as examples of MD runs.
(B) DEMOS (demo/)
Four examples of MD and FMO-MD simulations are given here:
one on BPTI and on PROT_DNA and on GAS_PEPT and the other on DNA_RNA.
They are intended to serve as examples of MD runs.
(C) DOCUMENT (doc/)
English document of PEACH.
(D) SOURCE PROGRAMS (src/)
* src/abinitmp contains sources for FMO.
* src/lib contains library for miscellaneous use.
* src/mkdbas contains sources for MKDBAS.
* src/mkmol contains sources for MKMOL.
* src/mkcor contains sources for MKCOR.
* src/mkpara contains sources for MKPARA.
* src/runmd contains sources for RUNMD. Should be linked with the libraries
* src/mdbndlib contains sources for bonding energy calculation programs.
* src/mdnonb_seq contains sources for nonbonded energy calculation programs.
* src/mdnonb_mpi contains sources for nonbonded energy calculation programs.
* src/mpirunfmo contains sources for MPIRUNFMO, analytical programs.
* src/mpirunmd contains sources for MPIRUNMD, analytical programs.
* src/analmd contains sources for ANALMD, analytical programs.
* src/MACHINE contains sources for machine dependent programs.
* src/misc contains sources for miscellaneous programs.
(E) DATABASE (data/)
Force field databases
Under the directory of data/dbase, you may find amino acid and
nucleotide databases used when constructing molecules.
The parameter data have been derived from the files distributed in
the AMBER HP:
We thank Professor P. A. Kollman of UCSF for allowing us to
redistribute the data.
(F) BENCHMARK (bench/)
results of benchmark tests on various machines.
(G) EXECUTABLES (EXE-W/)
Mail to: Nakata