From chemistry-request@server.ccl.net Fri Mar 22 03:20:38 2002 Received: from smtp.csc.fi ([193.166.0.99]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2M8Kap11735 for ; Fri, 22 Mar 2002 03:20:37 -0500 Received: from ISOSIRRI (dhcp-56.csc.fi [193.166.2.56]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with ESMTP id KAA17142; Fri, 22 Mar 2002 10:20:27 +0200 From: "Leif Laaksonen" To: "'Rick Venable'" , "'CCL'" Cc: "'Dr. Richard L. Wood'" , "'Jim Phillips'" Subject: RE: trajectory file conversion (update) Date: Fri, 22 Mar 2002 10:19:47 +0200 Message-ID: <002401c1d17a$54426fe0$3802a6c1@ISOSIRRI> MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.3416 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 In-Reply-To: I'm sorry but I made a mistake because I was in the believe that we talked about the representation in which the trajectories are saved on the the disk. The internal representation inside CHARMM/CHARMm is REAL*8 but the trajectories are saved on the disk in REAL*4. Am I right? -leif laaksonen -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net] On Behalf Of Rick Venable Sent: Friday, March 22, 2002 4:50 AM To: CCL Cc: Dr. Richard L. Wood; Jim Phillips Subject: CCL:trajectory file conversion (update) The f.p. difference I mentioned for CHARMM vs. CHARMm would seem to be historical; both use double precision (REAL*8) for coordinate and other f.p. numbers, and have for some time (years). I have not yet determined why I had problems with flipdcd previously-- but I plan to try again > from source (rather than pre-compiled Linux binary). I should also note that the trajectory transfer format (produced by DYNA FORMAT, converted back to binary via DYNA UNFORMAT) was changed at ca. CHARMM v. 27, in a way that lost backwards compatibility. It is strongly recommended that the same CHARMM version be used on both machine types in order to accomplish trajectory transfer via this mechanism. Finally, I should note that while CHARMM is not free, it is available as academically licensed source for a modest fee, a well crafted letter, and a bit of patience. Here's the information from the Karplus group: ----------------------------------------------------- We distribute the source code of the CHARMM program with documentation to individual academic research groups for a $600 licensing fee. CHARMM runs on a variety of UNIX workstations, including the SG Indigo machines. No graphics are necessary. The present version of the program being distributed is C28. The license is issued to the head of a laboratory or research group. Please send a letter with the full name and title of the professor in charge of your group and formal mailing address. Describe briefly the kind of research for which you intend to use the CHARMM program and the computers you will be using. The letter should be addressed to: The CHARMM Development Project Professor Martin Karplus Department of Chemistry & Chemical Biology 12 Oxford Street Harvard University Cambridge, Massachusetts 02138 ----------------------------------------------------- =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= -= 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 From chemistry-request@server.ccl.net Fri Mar 22 06:13:24 2002 Received: from dalton.quimica.unlp.edu.ar ([163.10.18.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2MBDLp16226 for ; Fri, 22 Mar 2002 06:13:23 -0500 Received: from bilbo.quimica.unlp.edu.ar (jubert4.quimica.unlp.edu.ar [163.10.18.18]) by dalton.quimica.unlp.edu.ar (8.10.2/8.11.2) with ESMTP id g2MBD8Y26320 for ; Fri, 22 Mar 2002 08:13:08 -0300 Message-Id: <5.1.0.14.0.20020322075733.009dd370@dalton.quimica.unlp.edu.ar> X-Sender: pis_diez@dalton.quimica.unlp.edu.ar X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 22 Mar 2002 08:13:52 -0300 To: chemistry@ccl.net From: Reinaldo Pis Diez Subject: MullPop: a program to do a Mulliken Population Analysis within Gaussian98 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear ccl'ers, Quite recently a post to the list was looking for some program to do the part of the MPA that Gaussian 9x doesn't. Well, I've just finished a program that I called MullPop and does exactly this task. You can have a look at http://www.quimica.unlp.edu.ar/cequinor/rpd_en.htm, under the "Software development" section, where you'll find a readme file describing the program and a tar.gz file to download the source if you wish. Regards, Reinaldo From chemistry-request@server.ccl.net Fri Mar 22 08:41:56 2002 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2MDftp19245 for ; Fri, 22 Mar 2002 08:41:55 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id IAA04904; Fri, 22 Mar 2002 08:41:46 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Fri, 22 Mar 2002 08:39:36 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GTD00M7WN45QQ@lvlmail.unitedcatalysts.com>; Fri, 22 Mar 2002 08:36:05 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Fri, 22 Mar 2002 08:40:04 -0500 Content-return: allowed Date: Fri, 22 Mar 2002 08:40:03 -0500 From: "Shobe, Dave" Subject: G98W: all solvents the same? To: "'CCL'" , "'help@gaussian.com'" Message-id: <157A51F55AAAD3119CD70008C7B1629D01C15AFD@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g2MDfup19246 Why do the following calculations using G98W's ICPM solvation model give the same results? #n geom=check guess=read chkbas scrf(isodensity,solvent=CCl4) #n geom=check guess=read chkbas scrf(isodensity,solvent=methanol) If "Epsi" in the output is the dielectric constant, it appears that both solvents have been replaced by water(?!) --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. From chemistry-request@server.ccl.net Fri Mar 22 08:52:07 2002 Received: from uranium.camsoft.com ([198.112.109.92]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2MDq7p19338 for ; Fri, 22 Mar 2002 08:52:07 -0500 Received: from potassium (172.17.3.55) by uranium.camsoft.com (Worldmail 1.3.167); 22 Mar 2002 08:52:02 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 22 Mar 2002 08:52:00 -0500 From: "Support" Subject: RE: {Talisma#033-946} Chem 3D Ultra 7.0 as a Gaussian interface. To: "Laurence Lavelle" , "CCL" Message-ID: <2002322_@TLM196749_@TLM> X-Mailer: Talisma Mail Component Version 2.5 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g2MDq7p19339 Just looking back at our correspondence with you, I have found that the three bugs you have reported and other suggestions have not been addressed in 7.0. The main things that have been added to Chem3D since 5.0 are a GAMESS interface and Tinker. Some bugs have been fixed, too. R&D is aware of the items you have reported and we hope to address them in a future version, but it is not clear when that will be. Regards, Rich Talbot Director, Technical Support CambridgeSoft support@cambridgesoft.com Do you want to know when software patches are available, the latest product problems and solutions, facts, tricks and tips, tidbits and more? Then sign up for our FREE technical support newsletter at: http://www.cambridgesoft.com/support/nl/new.cfm >-----Original Message----- >From: Laurence Lavelle[lavelle@mbi.ucla.edu] >Date: Thursday, March 21, 2002 06:54 PM >To: CCL[chemistry@ccl.net] >Subject: Chem 3D Ultra 7.0 as a Gaussian interface. > > >I tried using Chem 3D version 5 as a Gaussian interface some time back >but >it was full of bugs. > >Anyone having successful use of Chem 3D Ultra 7.0 as a Gaussian >interface ? >In particular for pdb files ? > >Thanks, >Laurence > > > From chemistry-request@server.ccl.net Thu Mar 21 22:02:37 2002 Received: from sina.com ([202.108.35.241]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g2M32ap02201 for ; Thu, 21 Mar 2002 22:02:37 -0500 Received: (qmail 21285 invoked by uid 99); 22 Mar 2002 02:58:49 -0000 Message-ID: <20020322025849.21284.qmail@sina.com> From: t218gy To: chemistry@ccl.net Subject: About charge analysis in Gaussian98 MIME-Version: 1.0 Date: Fri, 22 Mar 2002 10:58:49 +0800 X-Mailer: SinaMail 3.0Beta (FireToad) X-Priority: 3 Dear Sir, When I use the Guassian98 to do the charge analysis,the program need the radii of the Fe atom. I don't know how to input the the radii of Fe atom. My input line is belows: #P HF/STO-3G SCFCON=5 SCFCYC=300 EXTRABASIS POP=(MK,READRADII) IOP(6/33=2) Thanks in advance. Yi Gao Nanjing Univ. P.R.China ______________________________________ =================================================================== ÐÂÀËÃâ·Ñµç×ÓÓÊÏä (http://mail.sina.com.cn) ÐÂÀË·ÖÀàÐÅÏ¢£º¶þÊÖÊг¡×ßÒ»×ߣ¬¸Ã³öÊÖʱ¾Í³öÊÖ£¡ (http://classad.sina.com.cn/2shou/) From chemistry-request@server.ccl.net Fri Mar 22 08:38:41 2002 Received: from mmb1.vsnl.net.in ([202.54.1.72]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2MDcep19185 for ; Fri, 22 Mar 2002 08:38:40 -0500 Received: from bom2.vsnl.net.in (unknown [203.199.88.71]) by mmb1.vsnl.net.in (Postfix) with ESMTP id F28827D6F for ; Fri, 22 Mar 2002 19:08:24 +0530 (IST) Message-ID: <3C9B311D.3F09E57C@bom2.vsnl.net.in> Date: Fri, 22 Mar 2002 18:56:53 +0530 From: meenatul X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: Histidine X-Priority: 2 (High) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit To All Few days back by Dr David van der Spoel asked the question, regarding the state of histidine in proteins. I am also interested in knowing the answer. In what state Histidine should be modeled ? whether the two neutral isoforms or the protonated form? Especially if you are interested in using a physiological pH. Thanks Meena From chemistry-request@server.ccl.net Fri Mar 22 03:56:49 2002 Received: from omega.physchem.kth.se ([130.237.52.156]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2M8ump13258 for ; Fri, 22 Mar 2002 03:56:49 -0500 Received: from [130.237.52.42] (130.237.52.42) by omega.physchem.kth.se (MX V5.1-A An6n) with ESMTP; Fri, 22 Mar 2002 10:01:02 +0100 X-Sender: tore@omega.physchem.kth.se Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 22 Mar 2002 09:55:16 +0200 X-MX-Warning: Warning -- Invalid "To" header. To: peterc@server.ccl.net From: Tore Brinck Subject: CCL:StepSize CC: chemistry@ccl.net On Tue, 29 Jan 2002, Stanislav Ivan wrote: > I tried to reduce the step size during optimisation in gaussian98 - > opt=(StepSize=10) but but it doesn't work.I allways get the error > message about this keyword.But in the g98 manual I found exactly this > keyword. > All comments are appreciated. > > StepSize=N command doesn't work. Use IOp(1/8=N). Marek -= 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 Tore Brinck Physical Chemistry Royal Institute of Technology SE-100 44 Stockholm Phone: +46 8 790 82 10 Home: +46 8 655 85 52 Fax: +46 8 790 8207 Cell: +46 707 99 26 84 E-mail: tore@physchem.kth.se From chemistry-request@server.ccl.net Fri Mar 22 10:04:37 2002 Received: from sainfoin.saclay.cea.fr ([132.166.192.126]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2MF4ap21977 for ; Fri, 22 Mar 2002 10:04:36 -0500 Received: from araneus.SACLAY.CEA.FR (araneus.saclay.cea.fr [132.166.192.110]) by sainfoin.saclay.cea.fr (8.12.2/8.12.2/CEAnet-Internet.1.0) with ESMTP id g2MF5jG8027090 for ; Fri, 22 Mar 2002 16:05:46 +0100 (MET) Received: from silene.saclay.cea.fr (unverified) by araneus.SACLAY.CEA.FR (Content Technologies SMTPRS 4.2.10) with ESMTP id for ; Fri, 22 Mar 2002 16:01:03 +0100 Received: from pandora.saclay.cea.fr (pandora.saclay.cea.fr [132.166.23.28]) by silene.saclay.cea.fr (8.12.2/8.12.2/CEAnet-Interne.1.0) with ESMTP id g2MF2Wmp029946 for ; Fri, 22 Mar 2002 16:02:32 +0100 (MET) Received: from pandora.saclay.cea.fr (pandora.saclay.cea.fr [132.166.23.28]) by pandora.saclay.cea.fr (8.9.3/jtpda-5.3.2) with SMTP id QAA09090 for ; Fri, 22 Mar 2002 16:04:03 +0100 (MET) Message-Id: <200203221504.QAA09090@pandora.saclay.cea.fr> Date: Fri, 22 Mar 2002 16:04:03 +0100 (MET) From: Rodolphe Pollet Reply-To: Rodolphe Pollet Subject: PBC vs. cluster To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-MD5: G48115pc2a3F/aQegBQsbQ== X-Mailer: dtmail 1.2.1 CDE Version 1.2.1 SunOS 5.6 sun4u sparc Hi everyone, I am rather new in the field of classical Molecular Dynamics and i wonder what the pros and cons are between working on a very big cluster or choosing periodic boundary conditions. Don't you think there are some drawbacks in periodicity, especially if your potential is long-ranged ? Are big clusters really doomed because of Ewald correction or other tricks ? Are there any alternatives ? Thanks, Rodolphe Pollet. From chemistry-request@server.ccl.net Fri Mar 22 11:20:54 2002 Received: from chinon.cnrs-orleans.fr ([163.9.6.107]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2MGKrp24650 for ; Fri, 22 Mar 2002 11:20:53 -0500 Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.11.2/8.11.2) id g2MGKEh12895; Fri, 22 Mar 2002 17:20:14 +0100 X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f Sender: hinsen@chinon.cnrs-orleans.fr To: Rodolphe Pollet Cc: chemistry@ccl.net Subject: Re: CCL:PBC vs. cluster References: <200203221504.QAA09090@pandora.saclay.cea.fr> From: Konrad Hinsen Date: 22 Mar 2002 17:20:13 +0100 In-Reply-To: <200203221504.QAA09090@pandora.saclay.cea.fr> Message-ID: Lines: 18 User-Agent: Gnus/5.0808 (Gnus v5.8.8) Emacs/20.7 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Rodolphe Pollet writes: > I am rather new in the field of classical Molecular Dynamics and i > wonder what the pros and cons are between working on a very big > cluster or choosing periodic boundary conditions. Don't you think You don't say what kind of system you are working on. Basically you must decide decide whether you are more worried by artificial finite-size effects (e.g. surface tension) or by artificial periodicity. -- ------------------------------------------------------------------------------- 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 Fri Mar 22 11:24:13 2002 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2MGODp24827 for ; Fri, 22 Mar 2002 11:24:13 -0500 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id LAA18062; Fri, 22 Mar 2002 11:18:35 -0500 (EST) Date: Fri, 22 Mar 2002 11:18:35 -0500 From: Rick Venable To: Leif Laaksonen cc: "'CCL'" , "'Dr. Richard L. Wood'" , "'Jim Phillips'" Subject: RE: trajectory file conversion (update) In-Reply-To: <002401c1d17a$54426fe0$3802a6c1@ISOSIRRI> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 22 Mar 2002, Leif Laaksonen wrote: > I'm sorry but I made a mistake because I was in the believe that > we talked about the representation in which the trajectories are > saved on the the disk. The internal representation inside CHARMM/CHARMm > is REAL*8 but the trajectories are saved on the disk in REAL*4. > Am I right? Yes and no, it turns out. While coordinates are converted to REAL*4 for storage, unit cell data is stored as REAL*8 when the simulation used the CRYSTAL facility for periodic boundary conditions. For these trajectories, the 11th element of the 20 element INTEGER*4 header is set to 1, and the X, Y, and Z coordinate arrays are preceded by a 6 element REAL*8 array for each stored trajectory frame. I suspect that may be the root cause of the problems I had with flipdcd. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Fri Mar 22 11:41:27 2002 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2MGfRp25185 for ; Fri, 22 Mar 2002 11:41:27 -0500 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id LAA18040; Fri, 22 Mar 2002 11:35:50 -0500 (EST) Date: Fri, 22 Mar 2002 11:35:50 -0500 From: Rick Venable To: Rodolphe Pollet cc: chemistry@ccl.net Subject: Re: CCL:PBC vs. cluster In-Reply-To: <200203221504.QAA09090@pandora.saclay.cea.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 22 Mar 2002, Rodolphe Pollet wrote: > I am rather new in the field of classical Molecular Dynamics and i > wonder what the pros and cons are between working on a very big > cluster or choosing periodic boundary conditions. Don't you think > there are some drawbacks in periodicity, especially if your > potential is long-ranged ? Are big clusters really doomed because of > Ewald correction or other tricks ? Are there any alternatives ? There can be consequences of representing a non-periodic systems such as protein in aqueous solution with periodic boundary conditions, but there are also consequences to using a stochastic air:water boundary for a protein in a sphere of water as well. In both cases, an adequate thickness of solvent surrounding the solute is needed to reduce the impact of the boundary treament. In periodic systems, one can add ions to the solution to help screen out the longer range electrostatic effects, esp. when using Ewald methods. Particle-Mesh Ewald methods scale reasonably well on Linux clusters with CHARMM and AMBER, but as for most MD codes, a higher speed node interconnect such as Myrinet may be essential to get usable scaling on these types of clusters. Ethernet scaling under the 2.4 Linux kernel is particularly bad; the 2.2 kernel with the 'tcpfix' patch is highly recommended clusters using TCP/IP over ethernet. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Fri Mar 22 11:42:30 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2MGgUp25226 for ; Fri, 22 Mar 2002 11:42:30 -0500 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id LAA06339; Fri, 22 Mar 2002 11:42:24 -0500 (EST) Sender: richard@cornell.edu Message-ID: <3C9B5EEF.2887C4A0@cornell.edu> Date: Fri, 22 Mar 2002 11:42:23 -0500 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: Rodolphe Pollet CC: chemistry@ccl.net Subject: Re: CCL:PBC vs. cluster References: <200203221504.QAA09090@pandora.saclay.cea.fr> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Back when I did simulation of reactions in solution, we used truncated octahedral boundary conditions because these were supposedly less likely to bias calculations by introducing periodicity. Problem is that PBC's can actually introduce a significant computational overhead since they are called in the inner loops of the code. I'm especially interested in how people handle periodicity when they are simulating crystallization and do not want to bias the results by assuming a certain unit cell. Richard Gillilan MacCHESS Cornell University From chemistry-request@server.ccl.net Fri Mar 22 13:07:24 2002 Received: from mail-d.bcc.ac.uk ([144.82.100.24]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2MI7Op26822 for ; Fri, 22 Mar 2002 13:07:24 -0500 Received: from pop-c.ucl.ac.uk by mail-d.bcc.ac.uk with SMTP (Mailer) with ESMTP; Fri, 22 Mar 2002 18:07:12 +0000 Received: from ucl.ac.uk (chlorine.chem.ucl.ac.uk [128.40.76.17]) by pop-c.ucl.ac.uk (8.10.2+Sun/8.10.2) with ESMTP id g2MI6lm14333; Fri, 22 Mar 2002 18:06:47 GMT Sender: mb@ucl.ac.uk Message-ID: <3C9B712D.EC2B84A5@ucl.ac.uk> Date: Fri, 22 Mar 2002 18:00:13 +0000 From: Michael Brunsteiner Organization: University College London X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Richard Gillilan CC: Rodolphe Pollet , chemistry@ccl.net Subject: Re: CCL:PBC vs. cluster References: <200203221504.QAA09090@pandora.saclay.cea.fr> <3C9B5EEF.2887C4A0@cornell.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-UCL-MailScanner: Found to be clean Richard Gillilan wrote: > > I'm especially interested in how people > handle periodicity when they are > simulating crystallization and do not > want to bias the results by assuming a > certain unit cell. didn't read it myself but i think what you want could be in: BERNASCONI et al., JOURNAL OF PHYSICS AND CHEMISTRY OF SOLIDS 56 (3-4): 501-505 MAR-APR 1995 =================================================================== According to convention there is a sweet and a bitter, a hot and a cold, and according to convention, there is an order. In truth, there are atoms and a void. -- Democritus, 400 B.C. ------------------------------------------------------------------- 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 Fri Mar 22 10:28:42 2002 Received: from albert.unito.it ([130.192.119.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2MFSfp23285 for ; Fri, 22 Mar 2002 10:28:41 -0500 Received: (from root@localhost) by albert.unito.it (8.12.2/8.12.2) id g2MFSaiu001888 for chemistry@ccl.net; Fri, 22 Mar 2002 16:28:36 +0100 Received: from unito.it (chpc28.ch.unito.it [130.192.118.37]) by albert.unito.it (8.12.2/8.12.2) with ESMTP id g2MFSZ3H001847 for ; Fri, 22 Mar 2002 16:28:35 +0100 Message-ID: <3C9B4D27.78C1CCF@unito.it> Date: Fri, 22 Mar 2002 16:26:31 +0100 From: MSSC Organization: Dip. Chimica IFM X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: MSSC2002 - II circular and application form X-scanner: scanned by Inflex 1.0.9 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit International School of Advanced Study of the University of Torino Ab initio Modeling in Solid State Chemistry MSSC2002 http://www.chimifm.unito.it/teorica/mssc2002 September 8-13, 2002 -Torino, Italy Director: R. Dovesi, University of Torino The Theoretical Chemistry Group of the Torino University organizes a Summer School on the ab initio simulation of crystalline and defective solids. Ab initio modeling has become an ever-increasing area of interest in solid state chemistry and materials science. The software currently available for the quantum-mechanical study of electronic properties of crystalline systems satisfies some requirements that encourage its widespread use on the part of a rapidly growing community of non-specialized users (material scientists, crystallographers, geologists, ...). To fully exploit the potentialities of these powerful tools, however, is not an easy task, and an assisted introduction to their use from experts in the field may be beneficial. The MSSC School is addressed to PhD students with interests in solid state chemistry, physics, materials science, surface science, catalysis and provides an overview of the possibilities offered by ab initio quantum mechanical techniques when applied to characterize solid state materials. The present MSSC2002 School is intended as an introduction to the use of CRYSTAL, one of the most popular general-purpose programs for the study of crystalline solids, and the first which has been distributed publicly. Its aim is to give some general information about the fundamental issues behind the code, but especially to provide attendants with the practical skill for the clever use of the program in their field of interest. The new version of CRYSTAL will be used as a reference both in the morning lectures and in the afternoon tutorials. GENERAL INFORMATION Participation is restricted to 40 participants. The school will be held from September 8th to September 13th at the Chemistry Departments of the Torino University. Registration is scheduled on Sunday, September 8th at 14.00 at the University Guest House. The morning sessions will be devoted to lectures by experts. The afternoons will be dedicated to practical sessions. In the tutorials it will be shown how to obtain information concerning various observables using the CRYSTAL code. Participants will have the opportunity to present posters, that will be on display for the whole period and discussed during a special session. PARTICIPATION FEE The participation fee is 400,00 €. It includes: 1. accomodation at the University guest house in shared double room (seven nights, from Saturday 7th to Friday 13th September 2002, included) 2. lecture and tutorial notes 3. coffee break (morning) and lunch (from Monday 9th to Friday 13th September 2002) 4. all social events Notes: + Dinner is NOT included. + A limited number of single rooms will be available on request. An additional fee of 100,00 Euro is required. + For non resident attendants the partecipation fee is 250,00 Euro (items 2-3-4 above, included). For attendants who prefer an independent accomodation, the local organizing committee will not take care of hotel reservation. FINANCIAL AID A limited number of grants are available to partially cover participation costs (A participation contribution of 70,00 Euro is required). If funds are available, a maximum of 500,00 Euro will be given for refunding travel costs to participants from less favourite countries. Please note that preference in selecting participants will be given to eligible candidates who can guarantee travel coverage by their own local sources. Attendants applying for grants should provide a recommendation letter by their supervisor, group leader or a senior scientist. MSSC2002 HOME PAGE More detailed information (teachers, preliminary programme, ...) can be found at the MSSC2002 web site, which has been completely updated: http://www.chimifm.unito.it/teorica/mssc2002 The application form is either enclosed below in text format or can be downloaded from the MSSC2002 web site. The deadline is May 1st, 2002. Deadlines and Contact Information: Submission of application form by fax to +39-011-6707855: May 1st Notification of acceptance from the organizing committee: May 15th Submission of poster abstracts: July 15th E-mail: mssc@unito.it Telephone:+39 011 670 7561 Fax:+39 011 670 7855 Postal address: MSSC2002 Dipartimento di Chimica IFM Via Giuria, 5 I-10125 Torino, Italy *********** MSSC2002 - APPLICATION FORM ************* Please return this application form before May 1st, 2002, by fax to: MSSC2002 Dip.to di Chimica IFM - University of Torino Fax: +39-011-6707855 ------------------------------------------------------------------------------- Name: Surname: Gender: [ ] M [ ] F Organization: Position: [ ] Graduate student [ ] PhD student [ ] Postdoc [ ] Professor [ ] Research scientist [ ] Other: Address: City: Zip code: State: Country: Phone: Fax: e-mail: Are you a CRYSTAL user? [ ] Yes [ ] No Current scientific activities: Latest scientific pubblications (max 3): [ ] I will present a poster Request for financial assistance (Please provide a recommendation letter by your supervisor, group leader or senior scientist) Participation fee: [ ] Yes [ ] No (A limited number of grants are available to partially cover participation costs (70,00€ of contribution are required).) Travel costs: [ ] Total [ ] Partial [ ] None (If funds are available, a maximum of 500,00€ will be given for refunding travel costs to participants from less favourite countries. Please note that preference in selecting participants will be given to eligible candidates who can guarantee travel coverage by their own local sources.) Applicant's Signature : Date : -------------------------------------------------------------------------------- _____________________________________________________________________ For your security, this mail has been scanned and protected by Inflex