From owner-chemistry@ccl.net Wed Jun 14 02:41:00 2006 From: "Wai-To Chan chan]-[curl.gkcl.yorku.ca" To: CCL Subject: CCL: parameters Message-Id: <-31938-060614023042-9618-GxNOnsiHzeyJmQxccxyXWw^^^server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 14 Jun 2006 02:55:41 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan^^curl.gkcl.yorku.ca] <<<<<<<<<<<<<<<<<<<< Sent to CCL by: Ioana Cozmuta [ioana .. nas.nasa.gov] Hi CCL users, I am not sure if this is the best place to ask but I couldn't think of a better one. I want to do MD simulations of a gas formed by a mix of ATOMIC nitrogen and oxygen (N, O) interacting with a SiO2 surface at high temperatures (>800K). What would be the best empirical parameters (on- and off-diagonal) van der Waals interactions of N and O (again atoms and not molecules) to use? For the SiO2 surface I am using Morse stretch parameters from the MSQ force field by Demiralp et al. So far I tried the Dreiding parameters for O and N but I was wondering if anyone has done or knows of any refinement. Thank you, Ioana -- >>>>>>>>>>>>>>>>>>>>>>>>>> Did you try MOLECULAR DYNAMICS NEWS? I have no experience with MD simulation of an ensemble of atoms and molecules. I was at one time engaged in parameterization of molecular potential function, the type of potential for spectroscopic calculation and molecular trajectory simulation. I presume this is not the type of function used for MD simulation. Nonetheless I wonder if this type of function could be applicable for short time simulation of a small ensemble. I once parameterized a potential function for anionic hydroperoxy radical HO2-. The original functional is a complicated one including terms to describe long-range interaction. Somehow I obtained better results in terms of the error of fitting of the function to ab initio data points by using a simplified form of the function with all the long-range interaction components in the 3-body term eliminated. For an ensemble of a mix of O and N atoms at high temperature I assume the following two conditions: Absence of collisional stabilzation effect of the diatomics formed since there is no inert or non-reactive bath gas atoms and molecules. On account of the above condition any 3-body effect is negligible. I imagine in the MD simulation procedure there may be a way to correct for 3-body collision. For such a model I would guess accurate potential function for the diatomics is all you need. For a diatomic with distance R the functional form is like c1*exp(aR) --------- + Summation ci * exp(bR) * R (i=2,3...n) R Totally there are two exponential parameters and 4 coefficients for a homonuclear and 10 for a heteronuclear diatomic. Such a functional form is still way more complicated than a LJ or Morse potential. It should model very accurately the short range interaction. Although Van der Walls interaction is not explicitly described the asymptotic limit of the function should be correct as the fitting procedure can extrapolate the potential surface to the dissociation asymptotes. Assuming such a function is applicable to small scale MD simulation the parameterization of the diatomic potential should be doable. You will need ab initio data points for O--N, O--O and N---N. For system of this size accurate method like CCSD(T) in conjunction with largest basis sets can be used to calculate the potential curve extended to a bond length where long-range interatomic forces becomes significant. You may find similar type of accurate potential functions for O2, N2 and NO in literature. How accurate the resulting function would be in the region of the potential surface where the dynamics is governed by long-range interaction is I don't know. I just think it is reasonable to assume it has to be a lot more accurate than a Morse or LJ potential. Obviously I do not know if such diatomic potential can be incoporated to a model including interaction between the atoms and a surface. Wai-To Chan From owner-chemistry@ccl.net Wed Jun 14 05:27:01 2006 From: "Wai-To Chan chan|curl.gkcl.yorku.ca" To: CCL Subject: CCL: parameters Message-Id: <-31939-060614052342-23701-mibYdGG7lyitRYU5mjlIBw**server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 14 Jun 2006 05:49:03 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan|a|curl.gkcl.yorku.ca] An error in the functional form of the diatomic potential of Aguado and Paniagua from my previous message: <<<<<<<<<<<<<<<<<<<<<<<< c1*exp(aR) --------- + Summation ci * exp(bR) * R (i=2,3...n) R >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The products, aR and bR in the exponential factor cannot be positive. It should read exp(-aR) and exp(-bR). The parameters a and b are of course positive. Wai-To Chan From owner-chemistry@ccl.net Wed Jun 14 06:01:01 2006 From: "Tamas Gunda tgunda2005+/-puma.unideb.hu" To: CCL Subject: CCL: Reg: 2D to 3D conversion Message-Id: <-31940-060613032314-12573-9O/yc7DhgOtwZ71vwyNiNg[#]server.ccl.net> X-Original-From: "Tamas Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Tue, 13 Jun 2006 08:31:04 +0200 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda2005(~)puma.unideb.hu] The calculation of Gasteiger charges are described in: J.Gasteiger, M.Marsili: Tetrahedron, 36, 3219 (1980). The procedure supports only the H (D), N, O, S, F, P, S, Cl, Br and I atoms in sigma-bounded and nonconjugated pi-systems. Although mathematically not difficult, it is an iterative process, therefore manual calculation would be inconvenient. There are many shareware or even free applications which can do that, for example Mol2Mol (http://web.interware.hu/frenzy/mol2mol/index.html) Regards: Dr. Tamas E. Gunda University of Debrecen tgunda2005]_[puma.unideb.hu ----- Original Message ----- > From: "Anand Krishnamurthy anand{=}loyolacollege.edu" To: "Gunda, Tamas E " Sent: Monday, June 12, 2006 14:41 PM Subject: CCL: Reg: 2D to 3D conversion > Sent to CCL by: "Anand Krishnamurthy" [anand ~~ loyolacollege.edu] > Greeeting to one and all, > > I have really been benefitted extensively from an update to mechanise many > problems on computational chemistry. I would like to know the algorithm > involved in converting a two dimensional molecular structure data file > into a three dimensional one.Another question is that how do I calculate > manually gasteiger charges for small molecules and further can I automate > to place charges on all of the similar atoms in molecules. > > > Thanks and regards > Anand> > > From owner-chemistry@ccl.net Wed Jun 14 09:31:00 2006 From: "Wai-To Chan chan(!)curl.gkcl.yorku.ca" To: CCL Subject: CCL: parameters/correction Message-Id: <-31941-060614092722-4567-CE/tPBtwoDgvFNSwERF6Pw()server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 14 Jun 2006 09:52:40 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan+*+curl.gkcl.yorku.ca] I apologize for my multi-postings. I kept on showing the incorrect functional forms in my previous messages. Here is hopefully my last post on the subject. The diatomic potential function has the form: C_0*exp(-aR)/R + Summation{ C_i * rho^i} i=1...n rho=R*exp(-bR) I failed to show the summation in my previous posts as a polynomial. Wai-To Chan From owner-chemistry@ccl.net Wed Jun 14 11:44:00 2006 From: "Bing Dai bdai_1]^[hotmail.com" To: CCL Subject: CCL: question for cations Message-Id: <-31942-060614112913-6809-vv5UfkjHHTB0ToC2o2Ctrw|a|server.ccl.net> X-Original-From: "Bing Dai" Date: Wed, 14 Jun 2006 11:29:11 -0400 Sent to CCL by: "Bing Dai" [bdai_1*hotmail.com] Did anybody the a method which can calculate a system with two parts, one part with a positive charge and the other is neutral? The basic idea is that I just want to locate the charge to a certain atom of the system. Thanks Bing Dai bdai_1:hotmail.com From owner-chemistry@ccl.net Wed Jun 14 12:44:00 2006 From: "Young Leh youngleh]~[gmail.com" To: CCL Subject: CCL:G: ONIOM method Gaussian Error Message-Id: <-31943-060614124340-3394-ITwqf9hzcZYTHBxE0HWfAA..server.ccl.net> X-Original-From: "Young Leh" Date: Wed, 14 Jun 2006 12:43:36 -0400 Sent to CCL by: "Young Leh" [youngleh * gmail.com] Dear CCLer, I just started to run ONIOM calculation with Gaussian. Here is the error I ran into while running Gaussian jobs: Warning! Cu atom 34 has 11 valence electrons but only 4 basis functions. This is less than a minimal basis set! NAtoms= 429 NActive= 429 NUniq= 429 SFac= 1.00D+00 NAtFMM= 60 Big=T Simple Huckel Guess. NBasis=1446 NMin=1451 so simple Huckel guess is impossible. Error termination via Lnk1e in /usr/software/gaussian/g03/l401.exe at Thu Jun 8 12:11:39 2006. Job cpu time: 0 days 0 hours 2 minutes 58.5 seconds. File lengths (MBytes): RWF= 130 Int= 0 D2E= 0 Chk= 1 Scr= 1 My input file looks like: ONIOM(B3LYP/6-31G*:AM1) opt nosymm XXXX 0 1 Si -1 6.20200000 9.40000000 10.93900000 H Si -1 8.49400000 8.75500000 8.98300000 H Cu 0 7.727814 9.810079 11.801396 H : : : : : : X -1 XXX XXX XXX L X -1 XXX XXX XXX L X -1 XXX XXX XXX L X -1 XXX XXX XXX L Could somebody please help me out? Thanks and have a great day! Regards, Young Leh From owner-chemistry@ccl.net Wed Jun 14 13:19:01 2006 From: "John McKelvey jmmckel]~[attglobal.net" To: CCL Subject: CCL: Nortel VPN and Firewall Routers Message-Id: <-31944-060614123831-2655-PX4v3C/TQ73VJoZ2nhSmPw]~[server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 14 Jun 2006 12:30:19 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel+*+attglobal.net] CCLERs.. I post this issue here because I don't know where else to try, though it may be misplaced and should be elsewhere.. suggestions about that are also welcome! The setup: desktop PC with W2K/SP4, Norton firewall, Netgear firewall router, cable modem. The issue: First I always turn the Norton firewall off. Then, without the Netgear router I have no problem with the VPN client; however, with the Netgear router > 50% of the time I can get where I need to be, but I need to be able to get there >99% of the time! I get the classic 'contivity lost. plrase reconnect' I suspect that the Netgear configuration is the culprit here, and desperately need a/some suggestion(s) on how to deal with this issue [I'm just not a bits/bytes person :-) ] I'd be glad to take answers "off-line" is this is not a CCL type question. Many thanks! John McKelvey JMMcKel%x%attglobal.net 260-489-2160