From chemistry-request@server.ccl.net Mon Jan 20 04:54:47 2003 Received: from darius.ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0K9skV22393 for ; Mon, 20 Jan 2003 04:54:47 -0500 Received: from echo.ribotargets.com (echo [194.129.39.91]) by darius.ribotargets.com (SGI-8.9.3/8.9.3) with ESMTP id KAA69371; Mon, 20 Jan 2003 10:03:04 GMT Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 18aYZP-0002MO-00; Mon, 20 Jan 2003 09:50:19 +0000 Date: Mon, 20 Jan 2003 09:50:19 +0000 (GMT) From: Szilveszter Juhos To: Rolf Trinoga cc: chemistry@ccl.net Subject: Re: CCL:g98 for Linux and a new LINDA problem In-Reply-To: <200301171542.35317.trinoga@mpi-muelheim.mpg.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 17 Jan 2003, Rolf Trinoga wrote: > ldd shows that the link tries to use /opt/g98/util.so > util.so => /opt/g98/util.so (0x40013000) > Is there anybody with an idea ??? ldd /opt/g98/util.so ? nm /opt/g98/util.so | grep " U " ? Though not a magic bullet still :/ Cheers: Szilva From chemistry-request@server.ccl.net Mon Jan 20 03:49:54 2003 Received: from dsa.mpi-muelheim.mpg.de ([192.108.70.121]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0K8nrV08688 for ; Mon, 20 Jan 2003 03:49:53 -0500 Received: from pctritux ([172.17.104.6]) by dsa.mpi-muelheim.mpg.de (8.11.3/8.11.3) with ESMTP id h0K8nq3206436 for ; Mon, 20 Jan 2003 09:49:52 +0100 (MET) Content-Type: text/plain; charset="us-ascii" From: Rolf Trinoga Reply-To: trinoga@mpi-muelheim.mpg.de Organization: Max-Planck-Institut fuer Strahlenchemie To: chemistry@ccl.net Subject: Re: g98 for Linux and a new LINDA problem Date: Mon, 20 Jan 2003 09:53:30 +0100 User-Agent: KMail/1.4.3 MIME-Version: 1.0 Message-Id: <200301200953.30738.trinoga@mpi-muelheim.mpg.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h0K8nsV08689 thank you very much for all the information I got. It was a problem with the environment variables. I set them in .login and not in .cshrc it seems that .login will not be sourced using rsh. If the pgi directory is not mounted with NFS on each node, there is another "error while loading shared libraries: libpgc.so:" The workaround from Gaussian is to copy libpgc.so to Gaussian directory. regards Rolf Trinoga From chemistry-request@server.ccl.net Mon Jan 20 01:56:29 2003 Received: from col-msxproto2.col.missouri.edu ([128.206.3.152]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0K6uSV06948 for ; Mon, 20 Jan 2003 01:56:29 -0500 Received: from col-mailnode03.col.missouri.edu ([128.206.3.233]) by col-msxproto2.col.missouri.edu with Microsoft SMTPSVC(5.0.2195.5329); Mon, 20 Jan 2003 00:56:29 -0600 X-MimeOLE: Produced By Microsoft Exchange V6.0.6334.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8" Subject: about an error message in a charmm script output file Date: Mon, 20 Jan 2003 00:56:28 -0600 Message-ID: <2209664F1C807643B7FA01C8230C0F99034A4318@col-mailnode03.col.missouri.edu> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: about an error message in a charmm script output file Thread-Index: AcLAUQ5my/QeZp6PSn2h0tunPlAb+A== From: "Hu, Xiaohua" To: X-OriginalArrivalTime: 20 Jan 2003 06:56:29.0009 (UTC) FILETIME=[0EA0AC10:01C2C051] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id h0K6uVV06949 Dear CCL'ers, I am a newbee for charmm. When I run a charmm script file, I got an error message, and don't know how to fix it. My problem is: I try to read in 7000 frames in 4 trajectory files, and should get 7000 values. But I just got 6600 values, and job was terminated with an error message as following: " ***** LEVEL -1 WARNING FROM ***** " " ***** INPUT TRAJECTORY NOT SET UP. " If I just read in 6400 frames to get 6400 values, job done successfully. Does anybody know what's going on here ? Is there a limit to read in frames? Thank you so much my input file like this: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ...... ...... ...... set 8 0.0 label rholp ! SLAB DEFINITION AND COUNT ATOMS traj read coor stat sele bone1 end set 80 ?ZAVE ! OUTPUT TO FILE write title unit 80 * @8 @80 * ...... ...... ...... incr 8 by 1.0 if 8 le 7000.0 goto rholp stop >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the end of the output file: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ...... ...... ...... CHARMM> incr 8 by 1.0 Parameter: 8 <- "6600" CHARMM> if 8 le 7000.0 goto rholp Comparing "6600" and "7000.0". IF test evaluated as true. Performing command CHARMM> ! SLAB DEFINITION AND COUNT ATOMS CHARMM> traj read ***** LEVEL -1 WARNING FROM ***** ***** INPUT TRAJECTORY NOT SET UP. ****************************************** ...... ...... ...... >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best Regards Shawn Hu Chemistry Department University of Missouri, Columbia From chemistry-request@server.ccl.net Mon Jan 20 04:16:03 2003 Received: from gatekeeper.tripos.com ([192.160.145.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0K9G3V10122 for ; Mon, 20 Jan 2003 04:16:03 -0500 Received: (from uucp@localhost) by gatekeeper.tripos.com (8.11.6+Sun/8.11.6) id h0K9ELm01997 for ; Mon, 20 Jan 2003 03:14:21 -0600 (CST) Received: from cairo.tripos.com(172.20.176.21) by gatekeeper.tripos.com via csmap (V6.0) id srcAAA6kaG5d; Mon, 20 Jan 03 03:14:20 -0600 Received: (from nmalcolm@localhost) by cairo.tripos.com (SGI-8.9.3/8.9.3) id JAA71966; Mon, 20 Jan 2003 09:21:06 GMT Date: Mon, 20 Jan 2003 09:21:06 GMT Message-Id: <200301200921.JAA71966@cairo.tripos.com> X-Authentication-Warning: cairo.tripos.com: nmalcolm set sender to nmalcolm@tripos.com using -f From: "Nathaniel O.J. Malcolm" To: teo@epq.ime.eb.br CC: CHEMISTRY@CCL.NET In-reply-to: <001201c2be7b$b42e8e40$160ffea9@usuario> (teo@epq.ime.eb.br) Subject: Re: CCL:Cavity size in PCM Sender: nmalcolm@tripos.com Reply-To: nmalcolm@tripos.com Organization: Tripos UK Ltd. References: <001201c2be7b$b42e8e40$160ffea9@usuario> Teodorico, There is a paper from about 12 years ago by Orozzco et al. I think that deals with this question in the contect of the original MST overlapping sphere type cavity. Noj -- -------------------------------- Dr. N.O.J. Malcolm Software Support Scientist Tripos UK Ltd nmalcolm@tripos.com Tel +44 (0)1908 650020 Fax +44 (0)1908 650001 -------------------------------- Sybyl, Unity and other products are exclusive property of Tripos & are protected trademarks, copyrights, & patents as appropriate The information in this e-mail is confidential and may have associated legal obligations. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender. From chemistry-request@server.ccl.net Mon Jan 20 09:36:20 2003 Received: from far1.far.ub.es ([161.116.93.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0KEaJV28324 for ; Mon, 20 Jan 2003 09:36:20 -0500 Received: from jluque (luque2.far.ub.es [161.116.93.73]) by far1.far.ub.es (SGI-8.9.3/8.9.3) with SMTP id PAA80668; Mon, 20 Jan 2003 15:15:40 +0100 (CET) Message-ID: <003801c2c091$7b651c10$495d74a1@jluque> From: "F. J. Luque" To: "Teodorico Ramalho" Cc: References: <001201c2be7b$b42e8e40$160ffea9@usuario> Subject: Re: CCL:Cavity size in PCM Date: Mon, 20 Jan 2003 15:37:36 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0033_01C2C099.DBB581B0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6700 X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 This is a multi-part message in MIME format. ------=_NextPart_000_0033_01C2C099.DBB581B0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Teodorico, In the framework of the MST (Miertus-Scrocco-Tomasi) solvation model = developed at Barcelona=20 (closely related to the original Polarizable Continuum Model originally = formulated by Jacopo Tomasi at Pisa), we have been hardly working in the definition of the = solute/solvent interface for the calculation of the electrostatic and nonelectrostatic components = of the solvation free energy.=20 Regarding the nonelectrostatic terms, our latest version of the MST = model exploits van der Waals-like cavities (1). However, the solute/solvent interface = used for the=20 electrostatic term is built up by using a solvent-dependent factor that = scales Pauling's=20 atomic radii. Based on our studies, such a scaling factor varies from = 1.25 for solvation in water (2), to 1.50 in octanol (3), 1.60 in chloroform (4) and 1.80 in = carbon tetrachloride (5). Moreover, for charged compounds we found it necessary to reduce the = atomic radii of the atom(s) bearing the charge by around 10% (6). Hope this can help you. F. Javier Luque (1) Chem. Phys. 240 (1999) 253 (2) J. Comput. Chem. 15 (1994) 446 (3) J. Comput. Chem. 22 (2001) 1180 (4) J. Phys. Chem. 100 (1996) 4269 (5) J. Comput. Chem. 17 (1996) 806 (6) Chem. Phys. 182 (1994) 237 ----- Original Message -----=20 From: Teodorico Ramalho=20 To: CHEMISTRY@ccl.net=20 Sent: Friday, January 17, 2003 11:56 PM Subject: CCL:Cavity size in PCM Hi, =20 I would like to known if anyone to have some reference about the = cavity size effect in PCM (polarizable continuum model) in calculation = with molecules in form neutral and ionized. In other words, is there = great change in cavity radii when the molecule is in its ionized form = (+1 electron) ? Thanks by help. Best regardes, Teodorico C. Ramalho =20 ------=_NextPart_000_0033_01C2C099.DBB581B0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Teodorico,
 
In the framework of the MST=20 (Miertus-Scrocco-Tomasi) solvation model developed at Barcelona =
(closely related to the = original Polarizable Continuum Model originally formulated = by=20 Jacopo
Tomasi at Pisa), we have been hardly = working in the=20 definition of the solute/solvent interface
for the calculation of the = electrostatic and=20 nonelectrostatic components of the solvation free
energy.
Regarding the nonelectrostatic terms, = our latest=20 version of the MST model exploits
van der Waals-like cavities (1). = However, the=20 solute/solvent interface used for the
electrostatic term is built up by using = a=20 solvent-dependent factor that scales Pauling's
atomic radii. Based on our studies, = such a scaling=20 factor varies from 1.25 for solvation
in water (2), to 1.50 in octanol (3), = 1.60 in=20 chloroform (4) and 1.80 in carbon tetrachloride (5).
Moreover, for charged compounds we = found it=20 necessary to reduce the atomic radii of the
atom(s) bearing the charge by around = 10%=20 (6).
Hope this can help you.
 
F. Javier Luque
 
(1) Chem. Phys. 240 (1999) = 253
(2) J. Comput. Chem. 15 (1994) = 446
(3) J. Comput. Chem. 22 (2001) = 1180
(4) J. Phys. Chem. 100 (1996) = 4269
(5) J. Comput. Chem. 17 (1996) = 806
(6) Chem. Phys. 182 (1994) = 237
 
----- Original Message -----
From:=20 Teodorico=20 Ramalho
Sent: Friday, January 17, 2003 = 11:56=20 PM
Subject: CCL:Cavity size in = PCM

 Hi, =20

   =20 I would like to known if anyone to have some reference about the = cavity=20 size effect in PCM (polarizable continuum model) in calculation = with=20 molecules in form neutral and ionized. In other words, is there great = change=20 in cavity radii when the molecule is in its ionized form (+1 electron) = ?=20 Thanks by help.

 Best=20 regardes,

 Teodorico=20 C. Ramalho

 

------=_NextPart_000_0033_01C2C099.DBB581B0-- From chemistry-request@server.ccl.net Mon Jan 20 11:51:13 2003 Received: from umbi3.umbi.umd.edu ([136.160.7.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0KGpDe31877 for ; Mon, 20 Jan 2003 11:51:13 -0500 Received: from umbi.umd.edu ([129.6.112.59]) by umbi3.umbi.umd.edu (Netscape Messaging Server 4.15) with SMTP id H90UX500.DAI for ; Mon, 20 Jan 2003 11:53:29 -0500 Message-ID: <3E2C2B8F.FB2FCE31@umbi.umd.edu> Date: Mon, 20 Jan 2003 12:02:07 -0500 From: "Michael K. Gilson" Organization: CARB/UMBI X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: One more UPS question Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit MGE sells high capacity UPSs for considerably less than APC, for example. I'd be grateful for opinions of MGE from people who have experience with them. Thanks in advance, Mike From chemistry-request@server.ccl.net Mon Jan 20 18:44:04 2003 Received: from cascara.uvic.ca ([142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0KNi4e08705 for ; Mon, 20 Jan 2003 18:44:04 -0500 Received: from [24.65.168.211] ([24.65.168.211]) by cascara.uvic.ca (8.12.6/8.12.6) with ESMTP id h0I93YSw040742 for ; Sat, 18 Jan 2003 01:03:35 -0800 From: Roy Jensen To: chemistry@ccl.net Subject: Joke about computational chemistry... Date: Sat, 18 Jan 2003 01:03:53 -0800 Message-ID: <9g5i2v8i4llvhr4fjddmoka88vknab20lo@4ax.com> X-Mailer: Forte Agent 1.91/32.564 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-UVic-Virus-Scanned: OK - Passed virus scan by Sophos (sophie) on cascara X-Scanned-By: MIMEDefang 2.19 (www . roaringpenguin . com / mimedefang) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h0KNi4e08706 All I was hoping that someone could help me with a humorous poke at computational chemistry. I remember seeing it a few years ago, copying it down, and that's it... The quote goes something like: ********************************************************************* Three outcomes exist when solving the function x=f(x): 1) convergence to a fixed value 2) divergence 3) chaos [There might have been some comment that x=f(x) is an underlying function of chaos theory.] ********************************************************************* Any assistance in obtaining the actual statement and its reference would be GREATLY APPRECIATED! I will summarize your responses to CCL. Any other humorous comments will be included as well. Thanks, Roy Jensen