From chemistry-request@server.ccl.net Tue Oct 24 20:37:40 2000 Received: from jasper.uor.edu ([192.251.139.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA07804 for ; Tue, 24 Oct 2000 20:37:40 -0400 Received: by jasper.uor.edu id RAA0000022630; Tue, 24 Oct 2000 17:44:02 -0700 (PDT) Message-ID: <39F62A1B.243493C7@uor.edu> Date: Tue, 24 Oct 2000 17:32:27 -0700 From: Barbara Murray Organization: University of Redlands X-Mailer: Mozilla 4.5 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 CC: CHEMISTRY@ccl.net Subject: Re: CCL:Databases References: <39F5DADF.48979D4E@npd.ufpe.br> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit http://webbook.nist.gov/chemistry/ is a fairly good database for organic compounds. It may not have everything you want but it has some stuff. -- *********************************************************** Barbara Murray, Director bmurray@uor.edu Center for Science and Mathematics Phone: 909-793-2121 University of Redlands FAX: 909-793-2029 PO Box 3080, 1200 E. Colton Redlands, CA 92373-0999 From chemistry-request@server.ccl.net Tue Oct 24 20:51:43 2000 Received: from dns2.seanet.com (dns2.seanet.com [199.181.164.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA07869 for ; Tue, 24 Oct 2000 20:51:42 -0400 Received: from biggeek (dialup-63.214.11.87.Seattle1.Level3.net [63.214.11.87]) by dns2.seanet.com (8.9.3/8.9.0) with SMTP id RAA26847; Tue, 24 Oct 2000 17:51:00 -0700 (PDT) Message-ID: <006201c03e1d$025013f0$01808080@biggeek> From: "Mark A. Thompson" To: "env chem" , "spectroscopy" , "organic chem" , "nat prod" , "GAMESS" , "chem web" , "CCL" , "chem israel" , "chem ed2" , "chem ed" Cc: Subject: ArgusLab 2.0 Feedback Date: Tue, 24 Oct 2000 17:46:11 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_005D_01C03DE2.4BEE3720" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 This is a multi-part message in MIME format. ------=_NextPart_000_005D_01C03DE2.4BEE3720 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable (Apologies for the added bandwidth if you get this more than once). The response to ArgusLab 2.0 beta1 has been overwhelming. Thanks to all who have downloaded the program and are testing it. I encourage you to send feedback; especially on what you think about the molecule builder and other usability aspects of the UI. Click on this link to go directly to the ArgusLab 2.0 feedback page. http://www.seanet.com/~mthompson/ArgusLab/feedback.htm Mark Thompson ------=_NextPart_000_005D_01C03DE2.4BEE3720 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
(Apologies for the added = bandwidth if you=20 get this more than once).
 
The response to ArgusLab 2.0 = beta1 has=20 been overwhelming.
Thanks to all who have = downloaded the=20 program and are testing it.
 
I encourage you to send = feedback;=20 especially on what you think
about the molecule builder = and other=20 usability aspects of the UI.
 
Click on this link to go = directly to the=20 ArgusLab 2.0 feedback page.
http://ww= w.seanet.com/~mthompson/ArgusLab/feedback.htm
 
 
Mark Thompson
 
  ------=_NextPart_000_005D_01C03DE2.4BEE3720-- From chemistry-request@server.ccl.net Tue Oct 24 23:13:48 2000 Received: from mta1.263.net ([202.96.44.43]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA08539 for ; Tue, 24 Oct 2000 23:13:32 -0400 Received: by mta1.263.net (Postfix, from userid 60001) id 61A811C46CDB2; Wed, 25 Oct 2000 11:25:01 +0800 (CST) MIME-Version: 1.0 Message-Id: <39F6528D.12676@mta1> Date: Wed, 25 Oct 2000 11:25:01 +0800 (CST) From: "张 科春" To: chemistry@ccl.net Subject: help X-Priority: 3 X-Originating-IP: [159.226.54.60] Dear CCLers: I meet something interesting. Take for example: I use PM3 to MP2 to optimize H-CC-F...OCH3 system(C2v).When I use MOLDEN to read the output, I just see the H atoms vanished from the Z-amtrix. Where does the problem origiante? Can anyone help me? _____________________________________________ 首都在线--中国人的网上家园 http://www.263.net @263.net中国最大的在线邮局 http://freemail.263.net 中国人的在线购物乐园——263商城 http://shopping.263.net 网上留学咨询-中国教育服务网 http://edu.263.net/ From chemistry-request@server.ccl.net Wed Oct 25 04:19:01 2000 Received: from nottingham.ac.uk (jess.ccc.nottingham.ac.uk [128.243.40.193]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA10030 for ; Wed, 25 Oct 2000 04:19:01 -0400 Received: from gotham.ccc.nottingham.ac.uk ([128.243.40.48] helo=unix.ccc.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.13 #2) id 13oLlq-0002pV-00; Wed, 25 Oct 2000 09:18:50 +0100 Received: from granby ([128.243.40.43] helo=granby.ccc.nottingham.ac.uk) by unix.ccc.nottingham.ac.uk with esmtp (Exim 3.11 #2) id 13oLlp-0003VH-00; Wed, 25 Oct 2000 09:18:49 +0100 Date: Wed, 25 Oct 2000 09:18:48 +0100 (BST) From: Simon Cross X-Sender: pcxsc@granby.ccc.nottingham.ac.uk To: Barbara Murray cc: CHEMISTRY@ccl.net Subject: Re: CCL:Databases In-Reply-To: <39F62A1B.243493C7@uor.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII There is also the Cambridge Structural Database that should contain crystallographic information on a load of organic molecules, but I'm not sure of the URL. ----------------------------------------- Simon Cross School of Chemistry University of Nottingham tel. 0115 9514193 Email: pcxsc@nottingham.ac.uk From chemistry-request@server.ccl.net Wed Oct 25 05:18:13 2000 Received: from mail-d.bcc.ac.uk (mail-d.bcc.ac.uk [144.82.100.24]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA10312 for ; Wed, 25 Oct 2000 05:18:12 -0400 Received: from ucl.ac.uk (actually host chlorine.chem.ucl.ac.uk) by mail-d.bcc.ac.uk with SMTP (Mailer) with ESMTP; Wed, 25 Oct 2000 10:17:00 +0100 Sender: mb@ucl.ac.uk Message-ID: <39F6B234.51245F1A@ucl.ac.uk> Date: Wed, 25 Oct 2000 11:13:08 +0100 From: Michael Brunsteiner Organization: University College London X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: "Dr. Richard Wood" CC: chemistry@ccl.net Subject: Re: CCL:A Charmm question References: <39F5F524.57E654F5@cornell.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit "Dr. Richard Wood" wrote: > > Hi all > > Is there a better way to constrain bonds containing hydrogens when > heating other than using the command SHAKE? in case you mean better in terms of the required CPU-time: i'd employ a harmonic bond-stretching potential instead of SHAKE -- at least for the equilibration-phase -- since this is in many cases considerably faster than SHAKE, especially for (pseudo)cyclic molecules (like most water models are) mic =================================================== The Golden Rule of Arts and Sciences: He who has the gold makes the rules. "Why should we subsidize intellectual curiosity?" -Ronald Reagan --------------------------------------------------- Michael Brunsteiner Centre for Theoretical and Computational Chemistry University College London mailto:m.brunsteiner@ucl.ac.uk, http://www.ucl.ac.uk/~uccambr/ --------------------------------------------------- From chemistry-request@server.ccl.net Wed Oct 25 07:44:28 2000 Received: from sc2a.unige.ch (sc2a.unige.ch [129.194.48.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA11747 for ; Wed, 25 Oct 2000 07:44:28 -0400 Received: from chiphy.unige.ch ([129.194.52.184]) by sc2a.unige.ch (PMDF V5.2-32 #44957) with ESMTP id <01JVR8IUL2T60030SR@sc2a.unige.ch> for chemistry@ccl.net; Wed, 25 Oct 2000 13:44:13 MET-DST Date: Wed, 25 Oct 2000 13:37:18 +0200 From: Thomas Heine Subject: geometry optimisation within pbc Sender: Yves.Thomas@cellbio.unige.ch To: chemistry@ccl.net Message-id: <39F6C5EE.1074ED20@chiphy.unige.ch> Organization: University of Geneva MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.13 i686) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Dear CCLers, does anybody know an algorithm for geometry optimisation (cartesian) within periodic boundary conditions, e.g. in a simple rectangular super cell? Coordinates and the size of the super cell should be optimised. Thanks in advance Thomas Heine From chemistry-request@server.ccl.net Wed Oct 25 04:37:03 2000 Received: from rzcomm1.rz.tu-bs.de (root@rzcomm1.rz.tu-bs.de [134.169.9.107]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA10121 for ; Wed, 25 Oct 2000 04:37:02 -0400 Received: from tu-bs.de (pc1.org-chem.nat.tu-bs.de [134.169.19.154]) by rzcomm1.rz.tu-bs.de (8.9.3 (PHNE_18979)/8.9.3) with ESMTP id KAA18726; Wed, 25 Oct 2000 10:36:51 +0200 (METDST) Message-ID: <39F69BFC.EE5C5184@tu-bs.de> Date: Wed, 25 Oct 2000 10:38:20 +0200 From: "J. Grunenberg" X-Mailer: Mozilla 4.7 [de] (WinNT; I) X-Accept-Language: de MIME-Version: 1.0 To: Pedro Salvador , chemistry@ccl.net Subject: Re: CCL:g98 compiling error on Dec alpha References: <39F61188.7F01DD54@ouchem.chem.oakland.edu> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit > Dear CCLers > > I'm trying to install g98 on a Compaq Tru64 UNIX V5.0A (Rev. 1094) > machine with the Compaq C V6.1-019 and the Compaq Fortran V5.3-915 c > and f77 compilers, respectively > At the very beining of the installation i got this error on the cpp.c > file > > cc: Error: bsd/cpp.c, line 1542: In this statement, "MAXINCLUDE" is not > declared > >. (undeclared) > if (incend >= &incdir[MAXINCLUDE]) > ------------------------------------------^ > *** Exit 1 > Stop. > > Does anybody have experience on this platform? Any help will be > appreciated > > thank you very much in advance > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net Dear Pedro, modifying the alpha-osf1.make macro, >from CFLAGS = $(ALPHADEF) $(COPTFLAG) -trapuv to CFLAGS = $(ALPHADEF) $(COPTFLAG) -trapuv -std0 should correct this. Have a nice day, J鰎g -- Dr. J鰎g Grunenberg, Org. Chemie, Hagenring 30, 38106 Braunschweig email: Joerg.Grunenberg@tu-bs.de phone: +49 531 391 5252 URL: http://www.tu-bs.de/institute/org-chem/grunenberg/grunenberg.html From chemistry-request@server.ccl.net Wed Oct 25 06:27:14 2000 Received: from mailhost.curie.fr (burton.curie.fr [193.49.205.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA10585 for ; Wed, 25 Oct 2000 06:27:13 -0400 Received: from [193.48.227.167] (cm-1455-6659.curie.fr [193.48.227.167]) by mailhost.curie.fr (8.9.3/jtpda-5.3.3) with ESMTP id MAA03940 for ; Wed, 25 Oct 2000 12:27:00 +0200 (MET DST) Message-Id: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="============_-1239652872==_============" Date: Wed, 25 Oct 2000 12:26:59 +0200 To: chemistry@ccl.net From: Emmanuel Bertounesque Subject: Help with MOPAC --============_-1239652872==_============ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers I am a novice in Computational Chemistry. I am performing semiemperical AM1 calculations (SYBYL interface 6.5/QCPE program MOPAC) to determine the enthalpies of formation of two minimized* isomers, podophyllotoxin homolactone (trans-lactone) and picropodophyllin homolactone (cis-lactone), in order to compare the relative stability of these compounds. *Monte-Carlo multiconformational searches Here are the results with the following MOPAC set up: 1) Convergence: Normal and Precise 2) Optimization: Full 3) Other keyword: EF a) trans-lactone =3D=3D> dH=B0f =3D -251 Kcal/mol b) cis-lactone =3D=3D> dH=B0f =3D ? - Absence of cis-lactone.syb from the Files list. - Message in the file cis-lactone.out: "Internal coordinate derivatives do not reflect cartesian coordinate derivatives. To correct error, increase dihedral of atom 18 by 90 degrees". NB: the calculations were also done with no geometry optimization =3D=3D> dH=B0f =3D -217 Kcal/mol and partial optimization: all valence angles =3D=3D> calculation abondoned* all bonds =3D=3D> dH=B0f =3D -228 Kcal/mol all dihedral angles =3D=3D> dH=B0f =3D -226 Kcal/mol all bonds + all dihedral bonds =3D=3D> dH=B0f =3D -235 Kcal/mol all bonds + all dihedral bonds + all valence angles =3D=3D> calculation abon= doned* * Message: three atoms being used to define the coordinate of a fourth atom, whose bond angle is not zero or 180=B0, are in almost straight line. There is a highly probability that the coordinates of the atom will be incorrect. The faulty atom is atom number X. I don't know what to do now to access dH=B0f (cis) with full optimization. Any help would be greatly appreciated. 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N!!!!#J!#!')!!!))!!$D[J!!J!N""S##!!!!#J!#!)!!!!F1!!%!!!!9!'!!b!! $!%p)"3F"!!%!!JJ!!&V#!!!!"3%%!K!!!!#l!!!!"J%!!-)!!!!8!3!!!J3#!!J !+`3#!!%!!!!&J'8!!!!+!!)!B`!""J)!!J!%"J3!93!!!!8'"!"N!!!!!!!%J'B !!!!+!!)!C!!!!JJ!!#Ej!!"DrJ!!!!5!C`!!!!S!!J"P!!!##!!!'JB"!&Vq!!! !")"S!!!!#J!#!'B!!!))!!#0$!%!J!N"!!!%J'N!!!!+!!)!C`!!!JJ!!"S'!3# c&!%!!!5!DJ!!!!S!!J"S!!!##!!!*[N!!,-8!3!!"B"V!!!!#J!#!'N!!!B#!!) !!`B#!!%""!B%!')!!!!&"J3!CJ!!!!!!"B"X!!!!#J!#!'S!"!B%!'B!!!!&"J3 !C`!!!!!!"B"Y!!!!#J!#!'X!!!B#!!)!!`B#!!%""!B%!'F!!!!&"J3!D!!!!!! !"B"Z!!!!#J!#!'`!"!B%!'J!!!!&"J3!D3!!!!!!"B"[!!!!#J!#!'d!!!B#!!) !!`B#!!%""!B%!'N!!!!&"J3!DJ!!!!!!"B"`!!!!#J!#!'i!"!B%!')!!!!&"J3 !DJ!!!!!!")"a!!!!#J!#!'m!!!))!!#D$!%!'[-!"S#(!!!!#J!#!)8!!!F3!!% !!!!9!'!!b!!$!%p$5$-""`%!r`8(!3!$!!))!!!D%!%!C[B!"!)3!!!!#3%!!0d !!!!5!3!!pJ!!!!!%!J!&!!1!S!!!!!5!S3!!!!)%!J!)!!!!")#L!!!!+`3#!!- !!!!%J+8!!!!!"!)!$!!!!!@!S`!!!!3'"!#P!!!!"3B%!+%!!!!!!!@!T!!!!!3 '"!#K!!!!"3B%!+)!!!!!!!!!!!!&J()!!!!+!!)!F!!%"J3!C`!!!!8'"!"a!!! !!!!%J(-!!!!+!!)!F3!!!JJ!!)!C!3#!#3%'J)B!!!!+!!)!K!!!"a!!!3!!!"8 !B!$)!!-!6d0)-`8(!3!"!!))!!!!(3%!!!8""!)3!!!!&J%!!!B"!!!I!3!!(`% !!!!%!J!&!!1!TJ!!!!5!T`!!!!)%!J!)!!!!")#S!!!!+`3#!!-!!!!%J+X!!!! !"!)!$!!!!!@!U3!!!!3'"!#V!!!!"3B%!+F!!!!!!!@!UJ!!!!3'"!#R!!!!"3B %!+J!!!!!!!!!!!!&J(3!!!!+!!)!FJ!%"J3!D!!!!!8'"!"c!!!!!!!%J(8!!!! +!!)!F`!!!JJ!!*S-!3$Q(`%'J)8!!!!+!!)!J`!!"a!!!3!!!"8!B!$)!!-!6d0 )-`8(!3!"!!))!!!D%!%!CKX""!)3!!!!#3%!!"`"!!!5!3!!03%!!!!%!J!&!!1 !V!!!!!5!V3!!!!)%!J!)!!!!")#Z!!!!+`3#!!-!!!!%J,%!!!!!"!)!$!!!!!@ !V`!!!!3'"!#a!!!!"3B%!+d!!!!!!!@!X!!!!!3'"!#Y!!!!"3B%!+i!!!!!!!! !!!!&J(B!!!!+!!)!G!!%"J3!D3!!!!8'"!"e!!!!!!!%J(F!!!!+!!)!G3!!!JJ !!*VP!!$D(`%!!!5!H!!!!!S!!J"f!!!##!!!*Ym!!!!V!3D!L3!!!!S!!J#(!!! ($3!"!!!!&3"J!-J!!`"2!!))!!#QiJ!!J#B""!)3!!$cf`!!CLF"!22L!!"Q,J% !!!)%!J!)!!!!")"j!!!!#J!#!(F!!!))!!!cdJ!!!#X"!!!%J(S!!!!+!!)!H!! !!JJ!!-h,!!$D(`%!!!@!H`!!!!S!!J"j!!%'!J!'!!)'!3!""!B%!&-!!!!&"J3 !G`!!!!!!"B"m!!!!#J!#!(S!"!B%!(F!!!!&"J3!H!!!!!!!"B"p!!!!#J!#!(X !"!B%!(J!!!!&"J3!H3!!!!!!"B"q!!!!#J!#!(`!"!B%!(N!!!!&"J3!HJ!!!!! !"B"r!!!!#J!#!(d!!3B#!!B!!JB"!!%%"J3!9!!!!!8'"!"k!!!!!!!%J)!!!!! +!!)!IJ!!!JJ!!*Vb!!$D(`%'J)J!!!!+!!)!KJ!!"`d!!3!!!"8!B!$)!!-!6`! ##!!!'[B!!&SE!33#%!!!CZm!!%!F!3"QpJ!!3#-"!!!#"!)!#!!!!!@!J3!!!!S !!J"r!!!'!J!#!!3'"!"h!!!!"3B%!)!!!!!!!!!!"S#+!!!!#J!#!)J!!!FC!!% !!!!9!!!!b!!$!&4bB@jc,@aKBh4[EQ8#"`)!!3!!!JJ!!!!h!3!!EJ!%!K!!!!! `!3!!EJ!!!$F"!!#V!!!!"S#,!!!!#J!#!)N!!!FA!!%!!!!9!!!!b!!$!%0TFbe XB@0dEfjP!JF#!!%!!`F#!%%!!!))!!!!0J%!!28!"!)3!!!!,`%!!2B!!!!f!3! !*J%!!!!!!!!Vh!!!: --============_-1239652872==_============-- From chemistry-request@server.ccl.net Wed Oct 25 07:42:34 2000 Received: from post.tau.ac.il (post.tau.ac.il [132.66.16.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA11735 for ; Wed, 25 Oct 2000 07:42:33 -0400 Received: from post.tau.ac.il (pico.tau.ac.il [132.66.145.20]) by post.tau.ac.il (8.9.3/8.9.3) with ESMTP id NAA18981 for ; Wed, 25 Oct 2000 13:42:22 +0200 (IST) Sender: silviu@post.tau.ac.il Message-ID: <39F6C71D.83E379D2@post.tau.ac.il> Date: Wed, 25 Oct 2000 11:42:21 +0000 From: Zilberman Silviu Organization: TAU X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.10 i686) X-Accept-Language: en MIME-Version: 1.0 To: ccl Subject: curvature estimation Content-Type: multipart/mixed; boundary="------------F2EC3960EA38A289F2D014AA" This is a multi-part message in MIME format. --------------F2EC3960EA38A289F2D014AA Content-Type: multipart/alternative; boundary="------------CB9A9E1518C01F279C51D305" --------------CB9A9E1518C01F279C51D305 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, I am looking for an algorithm for estimation of local radii of curvature on a two dimensional square grid. The grid contains two domains, and the propagation should take into account the curvature of the interface between the domains. Any ideas or references? Thanks, Silviu. -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Zilberman Silviu School of Chemistry, Tel Aviv University Ramat Aviv, Tel-Aviv, Israel 61391 Phones 972-3-6407634 972-3-6409293 (fax 1) 972-3-6423765 (fax 2) mailto:silviu@post.tau.ac.il Home Page: http://pico.tau.ac.il %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% --------------CB9A9E1518C01F279C51D305 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all,

I am looking for an algorithm for estimation of local radii of curvature on a two dimensional square grid.
The grid contains two domains, and the propagation should take into account the curvature of the interface between the domains.
Any ideas or references?

Thanks, Silviu.
  

-- 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Zilberman Silviu

        School of Chemistry, Tel Aviv University
        Ramat Aviv, Tel-Aviv, Israel 61391

Phones
        972-3-6407634
        972-3-6409293 (fax 1)
        972-3-6423765 (fax 2)

mailto:silviu@post.tau.ac.il
Home Page: http://pico.tau.ac.il
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  --------------CB9A9E1518C01F279C51D305-- --------------F2EC3960EA38A289F2D014AA Content-Type: text/x-vcard; charset=us-ascii; name="silviu.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Zilberman Silviu Content-Disposition: attachment; filename="silviu.vcf" begin:vcard n:Zilberman;Silviu tel;work:972-3-6407634 x-mozilla-html:TRUE org:Tel Aviv University;School of Chemistry version:2.1 email;internet:silviu@post.tau.ac.il adr;quoted-printable:;;Tel Aviv University=0D=0ASchool of Chemistry;Tel Aviv;;69978;Israel x-mozilla-cpt:;-17216 fn:Silviu Zilberman end:vcard --------------F2EC3960EA38A289F2D014AA-- From chemistry-request@server.ccl.net Wed Oct 25 10:09:52 2000 Received: from admin.cnrs-orleans.fr (admin.cnrs-orleans.fr [163.9.1.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA12540 for ; Wed, 25 Oct 2000 10:09:51 -0400 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id QAA15060 ; Wed, 25 Oct 2000 16:08:43 +0200 (MET DST) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.9.3/8.9.3) id QAA23679; Wed, 25 Oct 2000 16:09:20 +0200 Date: Wed, 25 Oct 2000 16:09:20 +0200 Message-Id: <200010251409.QAA23679@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: hinsen@dirac.cnrs-orleans.fr To: Thomas.Heine@chiphy.unige.ch CC: chemistry@ccl.net In-reply-to: <39F6C5EE.1074ED20@chiphy.unige.ch> (message from Thomas Heine on Wed, 25 Oct 2000 13:37:18 +0200) Subject: Re: CCL:geometry optimisation within pbc References: <39F6C5EE.1074ED20@chiphy.unige.ch> > does anybody know an algorithm for geometry optimisation (cartesian) > within periodic boundary conditions, e.g. in a simple rectangular super > cell? Coordinates and the size of the super cell should be optimised. Any standard optimization algorithm should do it, you just add the size coordinate. And of course the potential energy must be calculated correctly for the periodic boundary conditions. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Oct 25 10:52:58 2000 Received: from ocswall01.fda.gov (ocswall01.fda.gov [198.77.181.7]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA12832 for ; Wed, 25 Oct 2000 10:52:58 -0400 Received: from cber.cber.fda.gov by ocswall01.fda.gov via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; 25 Oct 2000 14:47:26 UT Received: from nih.gov (cbmp24.cber.fda.gov) by CBER.CBER.FDA.GOV (PMDF V5.1-12 #D3363) with ESMTP id <01JVR2IIAGP48WYBH1@CBER.CBER.FDA.GOV> for chemistry@ccl.net; Wed, 25 Oct 2000 10:52:09 EDT Date: Wed, 25 Oct 2000 10:53:47 -0400 From: Rick Venable Subject: Re: CCL:A Charmm question To: Michael Brunsteiner Cc: "Dr. Richard Wood" , chemistry@ccl.net Reply-to: Rick_Venable@nih.gov Message-id: <39F6F3FA.2F8DB691@nih.gov> Organization: FDA/CBER/OVRR MIME-version: 1.0 X-Mailer: Mozilla 4.73 (Macintosh; U; PPC) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en References: <39F5F524.57E654F5@cornell.edu> <39F6B234.51245F1A@ucl.ac.uk> However, if you intend to use SHAKE later, then I'd advise using SHAKE throughout, esp. for water. Note that the TIP3 model requires the use of SHAKE to be consistent with the original published model. Michael Brunsteiner wrote: > > "Dr. Richard Wood" wrote: > > > > Hi all > > > > Is there a better way to constrain bonds containing hydrogens when > > heating other than using the command SHAKE? > > in case you mean better in terms of the required CPU-time: i'd employ a > harmonic bond-stretching potential instead of SHAKE -- at least for > the equilibration-phase -- since this is in many cases considerably > faster than SHAKE, especially for (pseudo)cyclic molecules (like most > water models are) > > mic > > =================================================== > The Golden Rule of Arts and Sciences: > He who has the gold makes the rules. > > "Why should we subsidize intellectual curiosity?" > -Ronald Reagan > --------------------------------------------------- > > Michael Brunsteiner > Centre for Theoretical and Computational Chemistry > University College London > mailto:m.brunsteiner@ucl.ac.uk, > http://www.ucl.ac.uk/~uccambr/ > --------------------------------------------------- > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net