From fgonzale@lauca.usach.cl Thu Mar 20 07:44:49 1997 Received: from ralun.usach.cl for fgonzale@lauca.usach.cl by www.ccl.net (8.8.3/950822.1) id GAA17713; Thu, 20 Mar 1997 06:32:02 -0500 (EST) Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by ralun.usach.cl (8.7.4/8.7.3) with ESMTP id HAA02375 for ; Fri, 21 Mar 1997 07:35:56 -0400 Received: (from fgonzale@localhost) by lauca.usach.cl (8.6.12/8.6.12) id IAA21720; Thu, 20 Mar 1997 08:33:23 -0400 Date: Thu, 20 Mar 1997 08:33:22 -0400 (CST) From: Fdo Danilo Gonzalez Nilo To: CHEMISTRY@www.ccl.net cc: Fdo Danilo Gonzalez Nilo Subject: Summary: Water Box (MD) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! It's the summary of the answers, about the following question: ************************************************************************** We are runnig a dynamic Calculation of a macroion with 8 positive charges in a water box, using PBC and a 30x30x30 cell, T=300 K, 50ps. We observe many water molecules going out from the box, during the process. We don't use any counterion. Is it normal that in the PBC condition, water molecules go out the cell? if not.... How can that be controlled? *********************************************************************** THANK YOU VERY MUCH to all the CCL is GREAT! ANSWERS: 1------------------------------------------------------------------ Hi, I'm a bit confused as to what you are asking. If you are using periodic boundary conditions then when the water molecules leave one side of the box they just return on the other side. When using PBC it should make no difference where you put the 'walls' of your box as you are hoping to simulate a bulk fluid. If I am misinterpreting your question please let me know and I'll try to answer it again. good luck, Marcus Martin Graduate Student Department of Chemistry, University of Minnesota marti108@gold.tc.umn.edu http://siepmann6.chem.umn.edu/~marcus 2-------------------------------------------------------------------- It all could depend on what software you're using. Bill Ross 3-------------------------------------------------------------------- Hi, PBC ensures the conserved number of particles and if it works correctly, the leaving water will enter from the opposite side of the box with the identical momentum. I am wondering which software are you using. One important thing doing simulation with the unbalancing chared system is the calculation of long-range interactions. For yours, Ewald summation must not be used. Usually, I used reaction-field method to cope with the long-range interactions if unbalance charge is present in the box. take care, Noy ---------------------------------------------------------------------------- Teerakiat Kerdcharoen, Ph.D. Profession: Lecturer and Information Technology Consultant Address: Department of Physics, Mahidol University, Bangkok 10400 Phone: 2461381 FAX 2461381 Cellular: 01-4906089 E-mail: noy@einstein.sc.mahidol.ac.th, noy@atc.atccu.chula.ac.th Homepage: http://www.sc.mahidol.ac.th/noy/ Research: Computer Aided Molecular Design (CAMD) ----------------------------------------------------------------------------- 3----------------------------------------------------------------------- Hi!! Yes, this is perfectly normal - as long as the water molecules come in again from the opposite side. And how could you prevent the water molecules from leaving the cell, anyway? You would have to make the cell boundary some kind of wall, where the molecules would be reflected. But this is exactly what you are trying to prevent with periodic boundary conditions - namely, a finite system that is influenced by boundary effects! On the other hand: If you are not applying any external force to the system, all molecules should leave the box in any direction with the same probability. SO if you have the impression that the molecules stream out through one side (and come in from the opposite side), then there is something wrong with your simulation. If you want to be sure about this, I think you should calculate the velocity auto-correlation function of the water molecules, which has to vanish within 1ps or so. If it does not, you are wittnessing this 'streaming effect'. good luck, gerald Gerald Loeffler PostDoc in Theoretical Biochemistry EMail: Gerald.Loeffler@univie.ac.at Phone: +43 1 79730 554 Fax: +43 1 7987153 SMail: I.M.P. - Research Institute of Molecular Pathology Dr. Bohr-Gasse 7 A-1030 Vienna AUSTRIA 4-------------------------------------------------------------------- Dear Mr Gonzalez, what program do you use? I know this problem from SYBYL 6.1 on Sun. There it was a bug. Within SYBYL 6.2 for Sun it is removed. But there exist other possibilities for the observed behaviour: 1. PBC allows a few water molecules to run a bit out of the box under one special condition. It depends on the minimum image convention normally used within PBC. However, this effects only less then 5 solvent molecules at one simulation step (from my observations), which leave the box only up to a distance lower than their molecular size. In a following step they return to their old place inside the box or are switched to the opposite side inside the box, if you watch a replay of the trajectories. 2. I guess you do the simulation within an NPT ensemble. Therefore the size of the box must be adjustable, it changes at everey simulation step. If you have the box dimension frozen, but you request an NPT ensemble, then many programs are confused. One possible result would be like you observed. 3. The box size should be related to the NBC. NBC should be not greater than 1/2 x boxlength. If your box is too small in relation to the NBC, it depends on the program how this is handled. Within SYBYL the box size will be enlarged without changing the number of particles, when NBC is greater than allowed. Sincerely yours B. Kallies ----------------------------------------------------- Dr. Bernd Kallies Institut fuer Physikalische und Theoretische Chemie Universitaet Potsdam Am Neuen Palais 10 14469 Potsdam GERMANY e-mail: kallies@serv.chem.uni-potsdam.de WWW : http://www.chem.uni-potsdam.de/~kallies/kallies.htm Tel : [+49] (0)331 / 977-1313 Fax : [+49] (0)331 / 977-1315 ----------------------------------------------------- 5---------------------------------------------------------------------- I'm not sure I understand the question. If you mean they go out one side of the cell and come in the other, then yes that is normal. That is why you use periodic boundary conditions. If you mean they go out and don't come back, then no that is not normal, and you are doing something wrong with your boundary conditions. Have I misunderstood the question? ------------- Visiting Research Instructor Steven J. Stuart U.S. Naval Academy stuart@brass.nadn.navy.mil 572 Holloway Rd., Mail Code 9B (410) 293-6636 Annapolis, MD 21402 fax: (410) 293-2218 6--------------------------------------------------------------------- What software are you running? I have had similiar problems before and it turned out that I had not defined something correctly. If you are using CHARMM I may be able to help. **************************************** Troy Wymore Department of Chemistry University of Missouri-Columbia Columbia, MO 65211 e-mail: chemtw@showme.missouri.edu http://www.missouri.edu/~chemtw/troy.html ***************************************** 7-------------------------------------------------------------------------- Hi, If you have water molecules comming in from the opposite direction, everything is fine. Istvan -- ************************************************* Istvan Enyedy The Catholic University of America Chemistry Department/ Malloney Hall Washington DC 20064 email istvan@bioorg.ee.cua.edu phone 202-319-5707 or 5349 fax 202-319-5381 ************************************************** ---------------------------------------------------------------------- Thanks a lot ... again Fernando Danilo Gonzalez N. University of Santiago of Chile Faculty of Chemistry and Biology Casilla 40, Correo 33, Santiago, Chile fono: (562) 681 2575 E-mail : fgonzale@lauca.usach.cl fax : (562) 681 2108 danilo@quimbio.usach.cl URL : http://quimbio.usach.cl/~danilo/ *************************************************************************x From PDu@synapticcorp.com Thu Mar 20 08:30:35 1997 Received: from S2 for PDu@synapticcorp.com by www.ccl.net (8.8.3/950822.1) id IAA18235; Thu, 20 Mar 1997 08:29:53 -0500 (EST) Received: by S2 from localhost (router,SLMAILNT V2.2); Thu, 20 Mar 1997 08:18:11 Eastern Standard Time Received: by S2 from S47.synaptic.com (38.232.56.47::mail daemon; unverified,SLMAILNT V2.2); Thu, 20 Mar 1997 08:18:11 Eastern Standard Time Comments: Authenticated sender is From: "Ping Du" To: CHEMISTRY@www.ccl.net Date: Thu, 20 Mar 1997 09:06:52 +0000 Subject: subscribe Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-Id: <19970320081811.09b4fb5e.in@S2> subscribe ccl From csg.admin@amgen.com Thu Mar 20 20:30:43 1997 Received: from castle-smtp.amgen.com for csg.admin@amgen.com by www.ccl.net (8.8.3/950822.1) id UAA23613; Thu, 20 Mar 1997 20:26:21 -0500 (EST) Received: by castle-smtp.amgen.com; id RAA01817; Thu, 20 Mar 1997 17:26:20 -0800 Received: from www-int.amgen.com(138.133.10.135) by castle-smtp.amgen.com via smap (V3.1) id xma001803; Thu, 20 Mar 97 17:25:55 -0800 Received: from iago.amgen.com (iago [138.133.10.249]) by www-int.amgen.com (8.8.5/8.8.5) with SMTP id RAA25378; Thu, 20 Mar 1997 17:25:54 -0800 (PST) Received: from amgen.com (amgengate) by iago.amgen.com (5.x/SMI-SVR4) id AA17863; Thu, 20 Mar 1997 17:25:46 -0800 Message-Id: Date: 20 Mar 1997 18:25:18 -0800 From: "csg admin" Subject: CCL-ZINDO Energy Units To: chemistry@www.ccl.net Cc: cache@pacificu.edu, jsokolow@tx.ncsu.edu X-Mailer: Mail*Link SMTP-QM 4.0.0 Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1"; Name="Message Body" Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by www-int.amgen.com id RAA25378 Mail*Link=AE SMTP CCL:ZINDO Energy Units Dear Modelers, Our group is interested in estimating the energy difference between singe= t and triplet and also doublet and quartet states of metal complexes using CACh= e ZINDO. Could somebody please tell me what the units of energy from Zindo= are, and how we can convert the energy differences into cm-1, or electron volt= s for instance. I will summarize any responses and post them to the list. Thanks, Jason --=20 _________________________________________________________________________= ______ Jason Lye, | =20 Dye Synthesis Research Group, | =20 College Of Textiles, Box 8301, | "Lifes' cheap, but North Carolina State University, | the accessories will kill you!" Raleigh, N.C. 27695 - 8301 | =20 | =20 Ph: (919) 515-6615 | =20 jlye@tx.ncsu.edu | =20 _________________________________________________________________________= ______ -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: jlye@tx.ncsu.edu -- Original Sender From: Address: jlye@unity.ncsu.edu CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordin= ator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net= 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html=20 ------------------ RFC822 Header Follows ------------------ Received: by amgen.com with ADMIN;20 Mar 1997 13:14:12 -0800 Received: from www-int.amgen.com by dorothy.amgen.com via ESMTP (940816.S= GI.8.6.9/921111.SGI) id MAA11911; Thu, 20 Mar 1997 12:59:02 -0800 Received: from castle-smtp.amgen.com (castle-smtp [138.133.19.51]) by www-int.amgen.com (8.8.5/8.8.5) with SMTP id MAA04514; Thu, 20 Mar 1997 12:59:02 -0800 (PST) Received: by castle-smtp.amgen.com; id MAA19153; Thu, 20 Mar 1997 12:59:0= 1 -0800 Received: from www.ccl.net(128.146.36.5) by castle-smtp.amgen.com= via smap (V3.1) id xma019144; Thu, 20 Mar 97 12:58:46 -0800 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.8.3/950822.1) id PAA22254; Thu, 20 Mar 1997 15= :43:40 -0500 (EST) X-Authentication-Warning: www.ccl.net: mail set sender to chemist= ry-request@www.ccl.net using -f Received: from ds10.tx.ncsu.edu for jlye@tx.ncsu.edu by www.ccl.net (8.8.3/950822.1) id OAA21628; Thu, 20 Mar 1997 14= :50:47 -0500 (EST) Received: by ds10.tx.ncsu.edu (5.65/Eos/C-U-09Sep93) id AA18819; Thu, 20 Mar 1997 14:50:32 -0500 From: "Jason Lye" Message-Id: <9703201450.ZM18817@unity.ncsu.edu> Date: Thu, 20 Mar 1997 14:50:19 -0500 X-Mailer: Z-Mail (3.2.1 15feb95) To: chemistry@www.ccl.net Subject: CCL:ZINDO Energy Units Cc: cache@pacificu.edu, jsokolow@tx.ncsu.edu Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk From csg.admin@amgen.com Thu Mar 20 20:30:51 1997 Received: from castle-smtp.amgen.com for csg.admin@amgen.com by www.ccl.net (8.8.3/950822.1) id UAA23583; Thu, 20 Mar 1997 20:22:22 -0500 (EST) Received: by castle-smtp.amgen.com; id RAA01622; Thu, 20 Mar 1997 17:22:17 -0800 Received: from www-int.amgen.com(138.133.10.135) by castle-smtp.amgen.com via smap (V3.1) id xma001606; Thu, 20 Mar 97 17:21:53 -0800 Received: from iago.amgen.com (iago [138.133.10.249]) by www-int.amgen.com (8.8.5/8.8.5) with SMTP id RAA25061 for ; Thu, 20 Mar 1997 17:21:52 -0800 (PST) Received: from amgen.com (amgengate) by iago.amgen.com (5.x/SMI-SVR4) id AA17724; Thu, 20 Mar 1997 17:21:49 -0800 Message-Id: Date: 20 Mar 1997 18:20:02 -0800 From: "csg admin" Subject: CCL-log P of FDOPA To: chemistry@www.ccl.net X-Mailer: Mail*Link SMTP-QM 4.0.0 Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1"; Name="Message Body" Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by www-int.amgen.com id RAA25061 Mail*Link=AE SMTP CCL:log P of FDOPA Dear Colleagues, I am looking for the logP value of FDOPA. Does anyone has calculated it once or know where to find this value eithe= r calculated or measured? Thanks for any help. Kind regards, Ilonka Guenther =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D Dr. Ilonka Guenther Service Hospital Frederic Joliot 4 Place de General Leclerc F- 91406 Orsay phone: +(33) (1) 69 86 77 52 fax: +(33) (1) 69 86 77 68 e-mail: guenther@uriens.shfj.cea.fr =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: guenther@shfj.cea.fr -- Original Sender From: Address: guenther@shfj.cea.fr CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordin= ator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net= 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html=20 ------------------ RFC822 Header Follows ------------------ Received: by amgen.com with ADMIN;20 Mar 1997 13:00:24 -0800 Received: from castle-smtp.amgen.com (castle-smtp [138.133.19.51]) by www-int.amgen.com (8.8.5/8.8.5) with SMTP id MAA03393 for ; Thu, 20 Mar 1997 12:45:17 -0800 (PST) Received: by castle-smtp.amgen.com; id MAA18510; Thu, 20 Mar 1997 12:45:1= 6 -0800 Received: from www.ccl.net(128.146.36.5) by castle-smtp.amgen.com= via smap (V3.1) id xma018506; Thu, 20 Mar 97 12:45:15 -0800 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.8.3/950822.1) id OAA21600; Thu, 20 Mar 1997 14= :43:36 -0500 (EST) X-Authentication-Warning: www.ccl.net: mail set sender to chemist= ry-request@www.ccl.net using -f Received: from nenuphar.saclay.cea.fr for guenther@shfj.cea.fr by www.ccl.net (8.8.3/950822.1) id OAA21197; Thu, 20 Mar 1997 14= :02:26 -0500 (EST) Received: from muguet.saclay.cea.fr by nenuphar.saclay.cea.fr (8.6.9/ CEANET-ROUTER-3.0) with ESMTP id UAA16545 for ; Thu, 20 Mar 1997 20:02:10 +0100 Received: from pendragon-int.shfj.cea.fr by muguet.saclay.cea.fr (8.6.9/ CEANET-ROUTER-3.0) with SMTP id UAA09754 for ; Thu, 20 Mar 1997 20:02:12 +0100 Received: by pendragon-int.shfj.cea.fr; id AA06117; Thu, 20 Mar 97 20:00:= 02 +0100 Received: from uriens.shfj.cea.fr(193.48.23.6) by pendragon-int.shfj.cea.= fr via smap (3.2) id xma006115; Thu, 20 Mar 97 19:59:52 +0100 Received: from [193.48.23.123] by shfj.cea.fr (SMI-8.6/PROTO-CEANET-3.0) with ESMTP id TAA01254 for ; Thu, 20 Mar 1997 19:59:43 +0100 X-Sender: guenther@193.48.23.36 Message-Id: Date: Thu, 20 Mar 1997 20:07:51 +0100 To: chemistry@www.ccl.net From: Ilonka Guenther Subject: CCL:log P of FDOPA Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk From csg.admin@amgen.com Thu Mar 20 21:30:42 1997 Received: from castle-smtp.amgen.com for csg.admin@amgen.com by www.ccl.net (8.8.3/950822.1) id UAA23697; Thu, 20 Mar 1997 20:45:20 -0500 (EST) Received: by castle-smtp.amgen.com; id RAA02637; Thu, 20 Mar 1997 17:45:18 -0800 Received: from www-int.amgen.com(138.133.10.135) by castle-smtp.amgen.com via smap (V3.1) id xma002621; Thu, 20 Mar 97 17:44:53 -0800 Received: from iago.amgen.com (iago [138.133.10.249]) by www-int.amgen.com (8.8.5/8.8.5) with SMTP id RAA26779; Thu, 20 Mar 1997 17:44:52 -0800 (PST) Received: from amgen.com (amgengate) by iago.amgen.com (5.x/SMI-SVR4) id AA18496; Thu, 20 Mar 1997 17:44:42 -0800 Message-Id: Date: 20 Mar 1997 18:40:17 -0800 From: "csg admin" Subject: CCL-ZINDO Energy Units To: chemistry@www.ccl.net Cc: cache@pacificu.edu, jsokolow@tx.ncsu.edu X-Mailer: Mail*Link SMTP-QM 4.0.0 Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1"; Name="Message Body" Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by www-int.amgen.com id RAA26779 Mail*Link=AE SMTP CCL:ZINDO Energy Units Dear Modelers, Our group is interested in estimating the energy difference between singe= t and triplet and also doublet and quartet states of metal complexes using CACh= e ZINDO. Could somebody please tell me what the units of energy from Zindo= are, and how we can convert the energy differences into cm-1, or electron volt= s for instance. I will summarize any responses and post them to the list. Thanks, Jason --=20 _________________________________________________________________________= ______ Jason Lye, | =20 Dye Synthesis Research Group, | =20 College Of Textiles, Box 8301, | "Lifes' cheap, but North Carolina State University, | the accessories will kill you!" Raleigh, N.C. 27695 - 8301 | =20 | =20 Ph: (919) 515-6615 | =20 jlye@tx.ncsu.edu | =20 _________________________________________________________________________= ______ -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: jlye@tx.ncsu.edu -- Original Sender From: Address: jlye@unity.ncsu.edu CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordin= ator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net= 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html=20 ------------------ RFC822 Header Follows ------------------ Received: by amgen.com with ADMIN;20 Mar 1997 13:48:51 -0800 Received: from castle-smtp.amgen.com (castle-smtp [138.133.19.51]) by www-int.amgen.com (8.8.5/8.8.5) with SMTP id NAA07227 for ; Thu, 20 Mar 1997 13:33:38 -0800 (PST) Received: by castle-smtp.amgen.com; id NAA20847; Thu, 20 Mar 1997 13:33:3= 8 -0800 Received: from www.ccl.net(128.146.36.5) by castle-smtp.amgen.com= via smap (V3.1) id xma020839; Thu, 20 Mar 97 13:33:20 -0800 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.8.3/950822.1) id PAA22248; Thu, 20 Mar 1997 15= :43:08 -0500 (EST) X-Authentication-Warning: www.ccl.net: mail set sender to chemist= ry-request@www.ccl.net using -f Received: from ds10.tx.ncsu.edu for jlye@tx.ncsu.edu by www.ccl.net (8.8.3/950822.1) id OAA21628; Thu, 20 Mar 1997 14= :50:47 -0500 (EST) Received: by ds10.tx.ncsu.edu (5.65/Eos/C-U-09Sep93) id AA18819; Thu, 20 Mar 1997 14:50:32 -0500 From: "Jason Lye" Message-Id: <9703201450.ZM18817@unity.ncsu.edu> Date: Thu, 20 Mar 1997 14:50:19 -0500 X-Mailer: Z-Mail (3.2.1 15feb95) To: chemistry@www.ccl.net Subject: CCL:ZINDO Energy Units Cc: cache@pacificu.edu, jsokolow@tx.ncsu.edu Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk