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<HTML>
<HEAD>
<TITLE>Acetylcholinesterase</TITLE>
</HEAD>
<BODY LINK="#00ee00" VLINK="#00ee00" BGCOLOR="#ffffff">
<FONT COLOR="#000000">
<H1><I>Acetylcholinesterase</I></H1>
<HR>
<IMG SRC="ache.gif">
<BR>
<HR>
More on the Acetylcholinesterase simulations using NWChem can be found in
<A HREF="http://www.npaci.edu/enVision/v14.1/mccammon.html#GFP">ENVISION</A>,
the NPACI/SDSC Quarterly.
<BR>
<BR>
<BR>
<BR>
Acetylcholinesterase molecular modeling and simulations studies:
<BR>
<BR>
M.K.Gilson, T.P.Straatsma, J.A.McCammon, D.R.Ripoll, C.H.Faerman,
P.H.Axelsen, I.Silman and J.L.Sussman, <BR>
<I>Open "Back Door" in a Molecular Dynamics Simulation of Acetylcholinesterase</I><BR>
<I>Science</I>, <B>263</B>,1276-1278 (1994).
<P>
S.Tara, T.P.Straatsma and J.A.McCammon,<BR>
<I>Acetylcholinesterase Unliganded and Complexed with Huperzine A: A Comparison
of Molecular Dynamics Simulations</I><BR>
<I>Biopolymers</I>, <B>50</B>, 35-43 (1999).
<P>
S.Tara, V.Helms, T.P.Straatsma, P.Taylor and J.A.McCammon,<BR>
<I>Molecular Dynamics of Mouse Acetylcholinesterase Complexed with Huperzine A</I><BR>
<I>Biopolymers</I>, in press.
</HTML>

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<HTML>
<HEAD>
<TITLE>Green Fluorescent Protein</TITLE>
</HEAD>
<BODY LINK="#00ee00" VLINK="#00ee00" BGCOLOR="#ffffff">
<FONT COLOR="#000000">
<H1><I>Green Fluorescent Protein</I></H1>
<HR>
<IMG SRC="gfp.gif">
<BR>
<HR>
More on the Green Fluorescent Protein simulation using NWChem can be found in
<A HREF="http://www.npaci.edu/enVision/v14.1/mccammon.html#GFP">ENVISION</A>, the
NPACI/SDSC Quarterly.
<BR>
<BR>
<BR>
<BR>
Green Fluorescent Protein molecular modeling and simulation studies:
<BR>
<BR>
V.Helms, E.F.Y.Hom, T.P.Straatsma, J.A.McCammon and P.Langhoff,<BR>
<I>Exciting Green Fluorescent Protein</I><BR>
<I>ACS Symposium Series</I>,<B>712</B>, 288-295 (1998).
<P>
V.Helms, T.P.Straatsma and J.A.McCammon,<BR>
<I>Internal Dynamics of Green Fluorescent Protein</I><BR>
<I>J.Chem.Phys.B</I>,<B>103</B>, 3263-3269 (1999).
<P>
</HTML>

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<HTML>
<HEAD>
<TITLE>HIV-1 Integrase</TITLE>
</HEAD>
<BODY LINK="#ffee00" VLINK="#00eeff" BGCOLOR="#ffffff">
<FONT COLOR="#000000">
<H1><I>HIV-1 Integrase</I></H1>
<HR>
<IMG SRC="hiv.gif">
<BR>
<HR>
<BR>
<BR>
<BR>
HIV-I Integrase molecular modeling and simulation studies:
<BR>
<BR>
R.D.Lins, J.M.Briggs, T.P.Straatsma, H.A.Carlson, J.Greenwald, S.Choe and J.A.McCammon,<BR>
<I>Molecular Dynamics Studies on the HIV-1 Integrase Catalytic Domain</I><BR>
<I>Biophys.J.</I>, <B>76</B>, 2999-3011 (1999).
<P>
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<HTML>
<HEAD>
<TITLE>NWChem Applications Page</TITLE>
</HEAD>
<BODY LINK="#0000e0" VLINK="#000e00" BGCOLOR="#ffffff">
<FONT COLOR="#000000">
<BR>
<BR>
<CENTER>
<H1><I>NWChem Applications</I></H1>
</CENTER>
<P>
<A HREF="gfp.html" TARGET="mainframe">Green Fluorescent Protein</A>. A molecular dynamics
simulation of wild type Green Fluorescent Protein from <I>Aequorea victoria</I> by Helms,
Straatsma and McCammon reveals remarkably rigid structure.
<P>
<A HREF="hiv1_int.html" TARGET="mainframe">HIV-1 Integrase</A>. Nanosecond simulations
were carried out of HIV-1 Integrase by Lins, Briggs, Straatsma,
Carlson, Greenwald, Choe and McCammon to determine the structure of the region in the
active site that was missing from published crystal structures.
<P>
<A HREF="ache.html" TARGET="mainframe">Acetylcholinesterase</A>. A molecular
dynamics study has been carried out by Tara, Helms, Straatsma and McCammon
on mouse acetylcholinesterase involving several nanosecond simulations of the
unliganded and huperzine-liganded enzyme.
<BR>
<P>
<P>
</HTML>

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<HTML>
<!-- DO NOT EDIT: this is a cleared public file -->
<HEAD>
<TITLE>NWChem availability</TITLE>
</HEAD>
<BODY BACKGROUND="backgrounds/state_map_2.jpg" BGCOLOR="FAEBD7">
<P><IMG SRC="images/nwchem/nwchem_logo.gif" ALT="NWChem - computational chemistry on parallel computers">
</P>
<HR>
At the time of writing the current version of NWChem was <I>1.2
alpha</I>. We do not plan to distribute the alpha or beta versions of
NWChem except to formal collaborators with specific needs. When the
distribution policy changes it will be widely announced. Until then,
if
<UL>
<LI> you have an existing collaboration with EMSL staff, or
<LI> you are interested in developing parallel computational chemistry
software within or around NWChem, and
<LI> have independent access to parallel computing resources, and
<LI> are able to share the results of your work with others, </UL>
then please contact your collaborators at PNNL or <A
HREF="support/support.html">nwchem-support@emsl.pnl.gov</A> for more
information.
<P> </P>
<UL><LI><A HREF="nwchem.html">Return to NWChem home page</A></UL>
<HR>
<ADDRESS>Prepared by RJ Harrison: Email: nwchem-support@emsl.pnl.gov.</ADDRESS>
</BODY>
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/html4/loose.dtd">
<html>
<!-- $Id: citation.html,v 1.1 2006-01-12 20:19:10 edo Exp $ -->
<head>
<meta http-equiv="Content-Type" content="text/html">
<meta name="Author" content="Mahin Hackler">
<link rel="stylesheet" type="text/css" href="shared/nwchem_basic.css">
<title>NWChem Citation</title>
</head>
<body bgcolor="#FFFFFF">
<table width="650">
<tr>
<td>
<br>
<table>
<tbody>
<tr>
<td align="left" width="325"><img src="images/nwchem_logo_dark.gif" border=0 width=200 alt="NWChem - computational chemistry on parallel computers"></td>
<td align="right" width="325" valign="bottom">
<a href="nwchem_main.html">NWChem Home</a> |
<a href="disclaimer.html">Security & Privacy</a> |
<a href="http://www.pnl.gov" target="_blank">PNNL</a>
</td>
</tr>
</tbody>
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<hr>
<h1>NWChem 4.7 Citation</h1>
<p><h2>NWChem 4.7 Production version</h2>
<p><b>In publicizing results obtained either in part or in full from use of the SOFTWARE,
USER shall place in a conspicuous location on all copies of the document containing the results,
the following acknowledgment:</b>
<p><b>Citation:</b><br>
Aprà, E.; Windus, T.L.; Straatsma, T.P.; Bylaska, E.J.; de Jong, W.; Hirata, S.;
Valiev, M.; Hackler, M.; Pollack, L.; Kowalski, K.; Harrison, R.; Dupuis, M.;
Smith, D.M.A; Nieplocha, J.; Tipparaju V.; Krishnan, M.; Auer, A.A.; Brown, E.;
Cisneros, G.; Fann, G.; Fruchtl, H.; Garza, J.; Hirao, K.; Kendall, R.; Nichols, J.;
Tsemekhman, K.; Wolinski, K.; Anchell, J.; Bernholdt, D.; Borowski, P.; Clark, T.;
Clerc, D.; Dachsel, H.; Deegan, M.; Dyall, K.; Elwood, D.; Glendening, E.; Gutowski, M.;
Hess, A.; Jaffe, J.; Johnson, B.; Ju, J.; Kobayashi, R.; Kutteh, R.; Lin, Z.;
Littlefield, R.; Long, X.; Meng, B.; Nakajima, T.; Niu, S.; Rosing, M.; Sandrone, G.;
Stave, M.; Taylor, H.; Thomas, G.; van Lenthe, J.; Wong, A.; Zhang, Z.;
"NWChem, A Computational Chemistry Package for Parallel Computers, Version 4.7" (2005),
Pacific Northwest National Laboratory, Richland, Washington 99352-0999, USA.</p>
<p>"High Performance Computational Chemistry: An Overview of NWChem a Distributed Parallel Application,"
Kendall, R.A.; Apra, E.; Bernholdt, D.E.; Bylaska, E.J.; Dupuis, M.; Fann, G.I.; Harrison, R.J.; Ju, J.;
Nichols, J.A.; Nieplocha, J.; Straatsma, T.P.; Windus, T.L.; Wong, A.T.; Computer Phys. Comm. 2000, 128, 260-283.</p>
<hr>
<p><h2>Modified version of NWChem</h2>
<p><b>In publicizing results obtained either in part or in full from use of a modified version of
NWChem, USER shall place in a conspicuous location on all copies of the document containing the
results, the following citations;</b></p>
<p><b>Citation:</b><br>
Aprà, E.; Windus, T.L.; Straatsma, T.P.; Bylaska, E.J.; de Jong, W.; Hirata, S.;
Valiev, M.; Hackler, M.; Pollack, L.; Kowalski, K.; Harrison, R.; Dupuis, M.;
Smith, D.M.A; Nieplocha, J.; Tipparaju V.; Krishnan, M.; Auer, A.A.; Brown, E.;
Cisneros, G.; Fann, G.; Fruchtl, H.; Garza, J.; Hirao, K.; Kendall, R.; Nichols, J.;
Tsemekhman, K.; Wolinski, K.; Anchell, J.; Bernholdt, D.; Borowski, P.; Clark, T.;
Clerc, D.; Dachsel, H.; Deegan, M.; Dyall, K.; Elwood, D.; Glendening, E.; Gutowski, M.;
Hess, A.; Jaffe, J.; Johnson, B.; Ju, J.; Kobayashi, R.; Kutteh, R.; Lin, Z.; Littlefield, R.;
Long, X.; Meng, B.; Nakajima, T.; Niu, S.; Rosing, M.; Sandrone, G.; Stave, M.; Taylor, H.;
Thomas, G.; van Lenthe, J.; Wong, A.; Zhang, Z.;
"NWChem, A Computational Chemistry Package for Parallel Computers, Version 4.7" (2005),
Pacific Northwest National Laboratory, Richland, Washington 99352-0999, USA. A modified version.</p>
<p>"High Performance Computational Chemistry: an Overview of NWChem a Distributed Parallel
Application", Kendall, R.A.; Aprà, E.; Bernholdt, D.E.; Bylaska, E.J.; Dupuis, M.; Fann, G.I.;
Harrison, R.J.; Ju, J.; Nichols, J.A.; Nieplocha, J.; Straatsma, T.P.; Windus, T.L.; Wong, A.T.
Computer Phys. Comm., 2000, 128, 260-283</p>
<hr>
<font size="0">
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<a href="support/faq/NWChem_FAQ.html">FAQ</a>
</center>
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<a href="support/support.html">Support</a> |
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<a href="http://www.emsl.pnl.gov/docs/mssg/index.html" target="_blank">Mol Sci. Soft. Group</a> |
<a href="citation.html">Citation</a>
</center>
</font>
<hr>
Contact: <a href="mailto:ms3distribution@emsl.pnl.gov">NWChem Support</a><br>
Updated: March 3, 2005
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<td align="left" width="325"><img src="images/nwchem_logo_dark.gif" border=0 width=200 alt="NWChem - computational chemistry on parallel computers"></td>
<td align="right" width="325" valign="bottom">
<a href="nwchem_main.html">NWChem Home</a> |
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<a href="http://www.pnl.gov" target="_blank">PNNL</a>
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<hr>
<h1>NWChem Contributors</h1>
<ul>
<li><a href="mailto:anchell@cache.fujitsu.com">James L. Anchell</a> </li>
<li><a href="mailto:Edoardo.Apra@pnl.gov">Edoardo Apr&agrave;</a>,
MS3 group, EMSL, PNNL. </li>
<li><a href="mailto:auer@sciborg.uwaterloo.ca">Alex A. Auer</a> </li>
<li><a href="mailto:bernholdtde@ornl.gov">David E. Bernholdt</a>,Oak
Ridge National Laboratory. </li>
<li><a href="mailto:pibcio@hermes.umcs.lublin.pl">Piotr Borowski</a> </li>
<li><a href="mailto:eric.bylaska@pnl.gov">Eric Bylaska</a>, EMSL,
PNNL. </li>
<li><a href="mailto:gerardo@sgi.com">Gerardo Cisneros</a>, Silicon
Graphics, S.A. de C.V. </li>
<li><a href="mailto:twclark@cs.uchicago.edu">Terry Clark</a> </li>
<li><a href="mailto:proddev@artek1.com">Daryl Clerc</a> </li>
<li><a href="mailto:h.dachsel@fz-juelich.de">Holger Dachsel</a> </li>
<li><a href="mailto:wibe.dejong@pnl.gov">Bert de Jong</a>, MSCF
Scientific Consulting Group, EMSL, PNNL. </li>
<li><a href="mailto:miles.deegan@hp.com">Miles J. Deegan</a> </li>
<li><a href="mailto:m_dupuis@pnl.gov">Michel Dupuis</a>, PNNL. </li>
<li><a href="mailto:dyall@schrodinger.com">Ken Dyall</a> </li>
<li><a href="mailto:dm_elwood@pnl.gov">David M. Elwood</a> </li>
<li><a href="mailto:fanngi@ornl.gov">George I. Fann</a>, Oak Ridge
National Laboratory. </li>
<li><a href="mailto:h.fruchtl@fle.fujitsu.com">Herbert A. Fr&uuml;chtl</a>,
Fujitsu </li>
<li><a href="mailto:jgo@xanum.uam.mx">Jorge Garza Olgu&igrave;n</a> </li>
<li><a href="mailto:ericg@chem.indstate.edu">Eric Glendening</a> </li>
<li><a href="mailto:maciej.gutowski@pnl.gov">Maciej S. Gutowski</a> </li>
<li><a href="mailto:mahin.hackler@pnl.gov">Mahin Hackler</a>, MS3
group, EMSL, PNNL. </li>
<li><a href="mailto:harrisonrj@ornl.gov">Robert J. Harrison</a>, Oak
Ridge National Laboratory. </li>
<li><a href="mailto:ahess@us.ibm.com">Anthony C. Hess</a> </li>
<li><a href="mailto:so.hirata@pnl.gov"> So Hirata</a>, MS3 group,
EMSL, PNNL. </li>
<li><a href="mailto:hirao@qcl.t.u-tokyo.ac.jp">K. Hirao</a>,
University of Tokyo. </li>
<li><a href="mailto:john.jaffe@pnl.gov">John E. Jaffe</a> </li>
<li><a href="mailto:johnson@quantumsim.com">Benny Johnson</a> </li>
<li><a href="mailto:jialin.ju@pnl.gov">Jialin Ju</a> </li>
<li><a href="mailto:rickyk@scl.ameslab.gov">Ricky A. Kendall</a>,
Scalable Computing Laboratory, Ames Laboratory, Ames, Iowa 50011
(formerly @ MS3 group). </li>
<li><a href="mailto:rika.kobayashi@anu.edu.au">Rika Kobayashi</a> </li>
<li><a href="mailto:R.Kutteh@ieee.org">Ramzi Kutteh</a>, Department of
Physics and Astronomy, John Hopkins University. </li>
<li><a href="mailto:zijing@excite.com"> ZiJin Lin</a> </li>
<li><a href="mailto:rj_littlefield@pnl.gov">Rik J. Littlefield</a> </li>
<li><a href="mailto:xipinglong@hotmail.com">XiPing Long</a> </li>
<LI><A HREF="mailto:Manojkumar.Krishnan@pnl.gov">Manoj Kumar Krishnan</A>
<li><A href="mailto:menggb@appliedbiosystems.com">Baoqi Meng </A> </li>
<li><a href="mailto:nakajima@qcl.t.u-tokyo.ac.jp"> T. Nakajima</a> </li>
<li><a href="mailto:nicholsja@ornl.gov">Jeff A. Nichols</a>, Oak
Ridge National Laboratory. </li>
<li><a href="mailto:j_nieplocha@pnl.gov">Jaroslaw Niep&#322;ocha</a> </li>
<li><a href="mailto:Lisa.Pollack@pnl.gov">Lisa Pollack</a>, MS3
group, EMSL, PNNL. </li>
<li><a href="mailto:sn72@georgetown.edu"> S. Niu</a> </li>
<li><a href="mailto:Alistair.Rendall@anu.edu.au">Alistair Rendall</a>,
Department of Computer Science, Australian National University. </li>
<li><a href="mailto:rosing@peakfive.com">Matt Rosing</a> </li>
<li><a href="mailto:gianni@edith.sublink.org">Giovanni Sandrone</a> </li>
<li><a href="mailto:smithdm@whitman.edu">Dayle Smith</a> </li>
<li><a href="mailto:msstave@cache.fujitsu.com">Mark S. Stave</a> </li>
<li><a href="mailto:tp_straatsma@pnl.gov">T. P. Straatsma</a>, MS3
group, EMSL, PNNL. </li>
<li><a href="mailto:htaylor@aventail.com">Hugh L. Taylor</a> </li>
<li><a href="mailto:gs_thomas@pnl.gov">Gregory S. Thomas</a> </li>
<li><a href="mailto:Vinod.Tipparaju@pnl.gov">Vinod Tipparaju</a> </li>
<li><a href="mailto:kirilt@ikazki01.chem.washington.edu">Kiril Tsemekhman</a> </li>
<li><a href="mailto:marat.valiev@pnl.gov">Marat Valiev</a>, MS3
group, EMSL, PNNL.</li>
<li><a href="mailto:joop@chem.ruu.nl">Joop van Lenthe</a> </li>
<li><a href="mailto:theresa.windus@pnl.gov">Theresa L. Windus</a>,
MS3 group, EMSL, PNNL. </li>
<li><a href="mailto:pg481@emsl.pnl.gov">Krzysztof Woli&#505;ski</a> </li>
<li><a href="mailto:atwong@nersc.gov">Adrian T. Wong</a>, NERSC. </li>
<li><a href="mailto:ZYZhang@lbl.gov">Zhiyong Zhang</a>, LBL. </li>
</ul>
<hr>
<font size="0">
<center>
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Contact: <a href="mailto:ms3distribution@emsl.pnl.gov">NWChem Support</a><br>
Updated: February 22, 2005
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<h1>Security & Privacy</h1>
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<p> This page initiates the mechanism for downloading either NWChem
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If you have any problems using this form or getting
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