From owner-chemistry@ccl.net Thu Jan 18 04:59:01 2007 From: "David van der Spoel spoel/a\xray.bmc.uu.se" To: CCL Subject: CCL: Gromacs: sp2-carbon Message-Id: <-33398-070118040408-16835-rd8ELvMq2lQkuN0FHuevVQ[A]server.ccl.net> X-Original-From: David van der Spoel Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 18 Jan 2007 09:10:43 +0100 MIME-Version: 1.0 Sent to CCL by: David van der Spoel [spoel**xray.bmc.uu.se] Edvin Erdtman edvin.erdtman()nat.oru.se wrote: > Sent to CCL by: "Edvin Erdtman" [edvin.erdtman~!~nat.oru.se] > Hello > I am trying to run a calculation of a membrane with a molecule inside it, containing a double bond. > I tried to use PRODRG, but it generates a strange topology file. The representations for sp2 carbons seems to be incorrect... > The carbons in the double bond get C and CR61 representations respectively. The bond length from CR61 to next (sp3) carbon become 0.139 nm, (as another double bond). > > When I am running the simulation, there is too much movements around the double bond, so there must be something strange here... > > I tried to change the representation of the "C" carbon to "CB" or "CR6" but it doesn't seem to help... > > Thankful for your help! > you're probably missing an improper dihedral, plz check your topology. Are you using the GORMOS96 force field? You might want to look into the Berger et al force field for lipids. -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel!=!xray.bmc.uu.se spoel!=!gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-chemistry@ccl.net Thu Jan 18 08:42:00 2007 From: "Tom F.A. de Greef t.f.a.d.greef(!)tue.nl" To: CCL Subject: CCL:G: Hindered Rotor Gaussian03 Message-Id: <-33399-070118043824-19898-VQuVDNvbAkjrLb6/gfNpGA[#]server.ccl.net> X-Original-From: "Tom F.A. de Greef" Date: Thu, 18 Jan 2007 04:38:20 -0500 Sent to CCL by: "Tom F.A. de Greef" [t.f.a.d.greef ~ tue.nl] Dear all, I want to report some deltaG values generated by a Gaussian03 job on a molecule of about 20 heavy atoms (B3LYP,6_311G+(d,p). However, I want to check if the assumptian that Gaussian03 makes are correct (the free rotor assumption). I requested a fequency job using the optimised geometry at the before mentioned level using these keywords: freq=hindered rb3lyp/6-311+g(d,p) geom=(connectivity,modredundant) "Geometry in Cartesian coordinates" It computes all the derivatives and computes the full mass-weighted force constant matrix. The calculation then starts a hindered rotation analysis: Internal coordinate list checked Check for planar centers 1 2 4 27 359.993 2 1 9 28 359.996 3 4 5 8 359.927 4 1 3 29 359.965 5 3 6 15 360.000 7 8 11 12 359.998 8 3 7 9 360.000 9 2 8 10 359.998 10 9 11 13 360.000 11 7 10 14 359.994 15 5 18 21 359.928 16 17 20 33 359.996 17 16 18 34 359.993 18 15 17 35 359.965 19 20 23 25 360.000 20 16 19 21 359.998 21 15 20 22 360.000 22 21 23 24 359.999 23 19 22 26 359.993 Check reduced barrier height. Cut-off : V/RT = 33.7561 Bond 3 - 5 frozen. Estimated reduced barrier height : V/RT = 37.5137 For a periodicity of : 2 Bond 5 - 15 frozen. Estimated reduced barrier height : V/RT = 37.5712 For a periodicity of : 2 Check for ring deformation Number of internal rotation degrees of freedom = 2 NNew= 92 NTest= 2 NB= 24 IFrz= 0 IBar= 2 ICyc= 0 Problem with the number of degrees of freedom Error termination via Lnk1e in /usr/opt/gaussian/g03/l716.exe I know that the method used by Gaussian03 to correct for hindered rotation is not always working (for example it works for butane but fails for methanol). For underlying thheory: P.Y. Ayala & H.B. Schlegel, JCP 108,2314 Best regards, Tom de Greef From owner-chemistry@ccl.net Thu Jan 18 09:18:01 2007 From: "Otello Maria Roscioni omr{}soton.ac.uk" To: CCL Subject: CCL:G: g03 density functionals for organometallic complexes Message-Id: <-33400-070117141047-2421-OJSpghFBbmnSkXBjUNEsyQ(-)server.ccl.net> X-Original-From: Otello Maria Roscioni Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 17 Jan 2007 18:33:15 +0000 MIME-Version: 1.0 Sent to CCL by: Otello Maria Roscioni [omr]![soton.ac.uk] Hello Adil, I am currently performing calculations on organometallics using Gaussian03 with different DFT functionals. In my experience, the MPW1K functional gives good results in calculating reaction barriers. You can find the route section for G03 in the Truhlar website: http://comp.chem.umn.edu/info/DFT.htm In this paper, you will find an interesting comparison of different DFT methods applied to the study of barrier heights for different reactions: J. Phys. Chem. A, 108, 7621 (2004). Good luck, Otello Adil Zhugralin zhugrali-*-bc.edu wrote: > Sent to CCL by: "Adil Zhugralin" [zhugrali-$-bc.edu] > > Dear all: > > I am trying to execute calculations on catalytic cycle involving ruthenium carbenes. I am experimentalist, but these calculations are essential for my research. Based on the little that I've read so far, DFT methods like B3LYP are generally not so good for organometallics. People in my field use either BP86 or PW91, but none of these are any good for calculating kinetic barriers. Recently Truhlar and co-workers disclosed a few new meta-hybrid-GGA's like M05 and M06, so I was wondering if anyone knows anything about them, that is to say, how reliable are they? Also, how would one go about obtaining them if necessary? And the last question: What basis sets would perform better for organometallics? (I'm trying to use 6-31G* on all atoms except Ru, for which I'm using Stuttgart/Dresden RECP). > > Thank you all! > > Adil> > > > > > > From owner-chemistry@ccl.net Thu Jan 18 21:20:00 2007 From: "Hunter, Ken ken.hunter^_^uleth.ca" To: CCL Subject: CCL:G: CCL question regarding comparison of Jaguar and Gaussian03 programs Message-Id: <-33401-070118154415-6857-AvL1uvvrFpGm3f0cBUM5GQ\a/server.ccl.net> X-Original-From: "Hunter, Ken" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C73B3C.3A080295" Date: Thu, 18 Jan 2007 13:07:06 -0700 MIME-Version: 1.0 Sent to CCL by: "Hunter, Ken" [ken.hunter-*-uleth.ca] This is a multi-part message in MIME format. ------_=_NextPart_001_01C73B3C.3A080295 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable We have been testing the applications of the Jaguar program and would like to incorporate the versatility of Jaguar to our computational chemistry group. However, one hesitation remains. When testing energies from our standard test molecules the energies we get from Jaguar are significantly different from our test calculations in Gaussian. Looking at the convergence criteria appears to be the same between the two programs and they have defined the basis sets the same. Differences seem to arise in optimizations and single points. We were curious if there any insights on how to reproduce Gaussian energies with Jaguar. Any assistance would be greatly appreciated. =20 Ken Hunter =20 ------_=_NextPart_001_01C73B3C.3A080295 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

We have been testing the applications of the Jaguar = program and would like to incorporate the versatility of Jaguar to our = computational chemistry group.  However, one hesitation remains.  When = testing energies from our standard test molecules the energies we get from = Jaguar are significantly different from our test calculations in Gaussian.  = Looking at the convergence criteria appears to be the same between the two = programs and they have defined the basis sets the same.  Differences seem to = arise in optimizations and single points.  We were curious if there any = insights on how to reproduce Gaussian energies with Jaguar.  Any assistance = would be greatly appreciated.

 

Ken Hunter

 

------_=_NextPart_001_01C73B3C.3A080295--