From owner-chemistry@ccl.net Fri Nov 5 04:30:01 2010 From: "Dillen, Jan jlmd(!)sun.ac.za JLMD(!)sun.ac.za" To: CCL Subject: CCL:G: Transition state calculation Message-Id: <-43079-101105023753-19823-VkVgULrYi8DiPPf+RZ0e8A^^^server.ccl.net> X-Original-From: "Dillen, Jan " Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 5 Nov 2010 08:37:30 +0200 MIME-Version: 1.0 Sent to CCL by: "Dillen, Jan [jlmd:_:sun.ac.za]" Henry, 1. Animate the vibrations associated with the negative frequencies. 2. Decide from the movements of the atoms which modes have nothing to do with the reaction coordinate that you associate with the SN2 reaction. 3. Distort the atoms with the eigenvectors of the unwanted negative frequencies (meaning that you add the eigenvector times a constant [0.5 usually works fine] to the coordinates). Alternatively, if these movements are e.g. rotations of alkyl groups, you can give them a kick by changing the torsion angles with e.g. MOLDEN. 4. Re-optimize with Opt(TS, NoEigenTest). Jan -----Original Message----- > From: owner-chemistry+jlmd==sun.ac.za/./ccl.net [mailto:owner-chemistry+jlmd==sun.ac.za/./ccl.net] On Behalf Of Henry Martinez hmartine * gmail.com Sent: 04 November 2010 22:00 To: Dillen, Jan Subject: CCL:G: Transition state calculation Sent to CCL by: "Henry Martinez" [hmartine###gmail.com] Hi everyone, I am running a Transition state calculation in Gaussian 03, using a b3lyp/ 3-21g freq opt:(ts, qst3,noigentest) for a simple SN2 over a primary alkyl halide (so I can start with something small then move to my systems). I am getting 2, some times 3 negative frequencies. I supposed to get only one. The transition state looks fine, I mean, it makes senses for this simple rx. But I would like to know how can I fix this problem of having more than one negative frequency. Thanks a lot for the help.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Nov 5 07:59:01 2010 From: "Jean Jules FIFEN julesfifen- -gmail.com" To: CCL Subject: CCL:G: Transition state calculation Message-Id: <-43080-101105065823-5272-pzofHYUuoUsaVGNkCJ7vLw,server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: multipart/alternative; boundary=000e0cd6b2aaf403d904944c25ee Date: Fri, 5 Nov 2010 11:58:01 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen[A]gmail.com] --000e0cd6b2aaf403d904944c25ee Content-Type: text/plain; charset=ISO-8859-1 If what suggest by Jan does not work, also try modifying the coordinates atom related to the last undesirable frequency mode and restart the computation. For that, you could use an atom editor from gausview, adding the opposite of amount of the higher deviations from zero on each coordinate. If this does not also work, try doing the computation computing analytical hessian at the first point or at any point if the previous does not success. J. Jules Fifen. On 5 November 2010 07:37, Dillen, Jan jlmd(!)sun.ac.za JLMD(!)sun.ac.za < owner-chemistry .. ccl.net> wrote: > > Sent to CCL by: "Dillen, Jan [jlmd:_:sun.ac.za]" > Henry, > > 1. Animate the vibrations associated with the negative frequencies. > 2. Decide from the movements of the atoms which modes have nothing to do > with the reaction coordinate that you associate with the SN2 reaction. > 3. Distort the atoms with the eigenvectors of the unwanted negative > frequencies (meaning that you add the eigenvector times a constant [0.5 > usually works fine] to the coordinates). Alternatively, if these movements > are e.g. rotations of alkyl groups, you can give them a kick by changing the > torsion angles with e.g. MOLDEN. > 4. Re-optimize with Opt(TS, NoEigenTest). > > Jan > > -----Original Message----- > > From: owner-chemistry+jlmd==sun.ac.za#ccl.net [mailto: > owner-chemistry+jlmd ==sun.ac.za#ccl.net] On > Behalf Of Henry Martinez hmartine * gmail.com > Sent: 04 November 2010 22:00 > To: Dillen, Jan > Subject: CCL:G: Transition state calculation > > > Sent to CCL by: "Henry Martinez" [hmartine###gmail.com] Hi everyone, I am > running a Transition state calculation in Gaussian 03, using a b3lyp/ 3-21g > freq opt:(ts, > qst3,noigentest) for a simple SN2 over a primary alkyl halide (so I can > start with something small then move to my systems). I am getting 2, some > times 3 negative frequencies. I supposed to get only one. The transition > state looks fine, I mean, it makes senses for this simple rx. But I would > like to know how can I fix this problem of having more than one negative > frequency. Thanks a lot for the help.http://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > -- Jean Jules FIFEN, +237 75 21 61 39 +237 94 67 65 05 University of Ngaoundere, PO.BOX 454 Ngaoundere --000e0cd6b2aaf403d904944c25ee Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
If what suggest by Jan does not work, also try modifying t= he coordinates atom related to the last undesirable frequency mode and rest= art the computation. For that, you could use an atom editor from gausview, = adding the opposite of amount of the higher deviations from zero on each co= ordinate.
If this does not also work, try doing the computation computing analytical = hessian at the first point or at any point if the previous does not success= .

J. Jules Fifen.

On 5 November 2= 010 07:37, Dillen, Jan jlmd(!)sun.ac.za JL= MD(!)sun.ac.za <owner-chemistry .. ccl.net> wrote:

Sent to CCL by: "Dillen, Jan [jlmd:_:sun.ac.za]" <JLMD:_:sun.ac.za>
Henry,

1. Animate the vibrations associated with the negative frequencies.
2. Decide from the movements of the atoms which modes have nothing to do wi= th the reaction coordinate that you associate with the SN2 reaction.
3. Distort the atoms with the eigenvectors of the unwanted negative frequen= cies (meaning that you add the eigenvector times a constant [0.5 usually wo= rks fine] to the coordinates). Alternatively, if these movements are e.g. r= otations of alkyl groups, you can give them a kick by changing the torsion = angles with e.g. MOLDEN.
4. Re-optimize with Opt(TS, NoEigenTest).

Jan

-----Original Message-----
> From: owner-chemistry+jlmd=3D=3Dsun.ac.za#ccl.net [mailto:owner-chemistry+jlmd=3D=3Dsun.ac.za#ccl.net] On Behalf Of Henry Martinez = hmartine * gmail.com
Sent: 04 November 2010 22:00
To: Dillen, Jan <jlmd#sun= .ac.za>
Subject: CCL:G: Transition state calculation


Sent to CCL by: "Henry =A0Martinez" [hmartine###gmail.com] Hi everyone, I am running a Tr= ansition state calculation in Gaussian 03, using a b3lyp/ 3-21g freq opt:(t= s,
qst3,noigentest) for a simple SN2 o= ver a primary alkyl halide (so I can start with something small then move t= o my systems). I am getting 2, some times 3 negative frequencies. I suppose= d to get only one. The transition state looks fine, I mean, it makes senses= for this simple rx. But I would like to know how can I fix this problem of= having more than one negative frequency. Thanks a lot for the help.http= ://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub= _unsub.shtmlhttp://www.ccl.net/spammers.txt


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--
Jean Jules = FIFEN,
+237 75 21 61 39
+237 94 67 65 05
University of Ngaoundere,=
PO.BOX 454 Ngaoundere
--000e0cd6b2aaf403d904944c25ee-- From owner-chemistry@ccl.net Fri Nov 5 09:17:38 2010 From: "Sayed Mesa elsayed.elmes++yahoo.com" To: CCL Subject: CCL:G: Antiferromagentism of dinulear transition metal complexes Message-Id: <-43081-101102154927-6273-iSDXAwG9+Y3dcfOOjtc64Q_._server.ccl.net> X-Original-From: "Sayed Mesa" Date: Tue, 2 Nov 2010 15:49:25 -0400 Sent to CCL by: "Sayed Mesa" [elsayed.elmes{:}yahoo.com] Dear All: I have measured the magnetism of some dinulear transition metal complexes, where transition metals are Co2+, Ni2+ & Cu2+. Some complexes shows strong antiferromagentism and some others shows weak antiferromagentism while the remaining are ferromagentic. I would like to optimize the geometries of these complexes with DFT (Gaussian), but I am confused how can I define the spin of the dinuclear complexs. By the way, the total number of eletrons of complexes is even in all cases. I know that diCobalet complex may have spin state of 1, 3, 5 or 7, while diNikel complex have have spin states 1, 3 or 5. For dicopper, the spin state may have 1 or 3. My question: Should I optimize the geometries of all probabilities of spin states and then choose the lowest energy among them. This scenario is valid? Thanks in advance, Sayed From owner-chemistry@ccl.net Fri Nov 5 09:19:45 2010 From: "Arun Venkatnathan arunv1973*|*yahoo.com" To: CCL Subject: CCL: Dispersion, DFT and NWChem Message-Id: <-43082-101103121531-31288-fdFlRZZXacmbtKhw5N3s9g-,-server.ccl.net> X-Original-From: Arun Venkatnathan Content-Type: multipart/alternative; boundary="0-842311364-1288800925=:83490" Date: Wed, 3 Nov 2010 09:15:25 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Arun Venkatnathan [arunv1973:+:yahoo.com] --0-842311364-1288800925=:83490 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCLers,=20 Can anyone suggest most recommended functionals in DFT for treating dispers= ion accurately using the functionals available in NWChem. The system used f= or my study is clathrates. E.g, a gas molecule trapped by water molecules. Thanks, Dr. Arun Venkatnathan Assistant Professor, Chemistry Indian Institute of Science Education and Research, Pune Pashan 411021=A0 India E-mail: arun[]iiserpune.ac.in =0A=0A=0A --0-842311364-1288800925=:83490 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear CCLers,

Can anyone suggest most = recommended functionals in DFT for treating dispersion accurately using the= functionals available in NWChem. The system used for my study is clathrate= s. E.g, a gas molecule trapped by water molecules.

Thanks,
Dr. Ar= un Venkatnathan
Assistant Professor, Chemistry
Indian Institute of Sc= ience Education and Research, Pune
Pashan 411021  India
E-mail: = arun[]iiserpune.ac.in


=0A=0A --0-842311364-1288800925=:83490-- From owner-chemistry@ccl.net Fri Nov 5 09:26:01 2010 From: "Jan Labanowski janl\a/speakeasy.net" To: CCL Subject: CCL: You may see some repeated messages on CCL Message-Id: <-43083-101105092418-14128-SKTXsQDzZrfzNayX9s7ARQ\a/server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Fri, 05 Nov 2010 09:23:55 EDT MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl:speakeasy.net] I had to resent two messages to CCL after a power outage two days ago. So you may get two copies. I discovered that they were not sent to all subscribers since the power went out before the batch job finished. Jan From owner-chemistry@ccl.net Fri Nov 5 15:18:00 2010 From: "Venable, Richard (NIH/NHLBI) E venabler(a)nhlbi.nih.gov" To: CCL Subject: CCL: Release of R.E.D. Server 2.0 Message-Id: <-43084-101105151335-10949-dd/qhvoo6wlJ+yQz5t5gKw(!)server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 5 Nov 2010 15:12:55 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler__nhlbi.nih.gov] I've read through the paper and the two specific CHARMM citations, and have to admit my first response over-assumed a reliance on RESP charges. However, I am still concerned about the claim to be to produce complete force field libraries for CHARMM, which I initially interpreted as ready-to-use residues in the proper topology file format, which wasn't the case. I believe a claim of being able to produce entire CHARMM compatible force field libraries should be demonstrated much more completely. This quote from the cited paper itself raises question about the level of CHARMM and OPLS compatibility: "Indeed, RESP and ESP charge values derived using R.E.D. are fully compatible with Amber and GLYCAM force fields, (40-47) and can be used in CHARMM and OPLS force field based simulations as well. (17-20)" References 19 and 20 are not really demonstrations of the exact use of R.E.D., but use CHELPG for the initial charges, which are further adjusted for CHARMM compatibility. Reading further, it seems the burden of choosing the correct LJ types, and thereby the mapping to angle and dihedral terms, is left completely up to the end user, which I see as a major weakness. Thus, the type independence may pose a problem, in that novel bonding geometries can be created for which there are no angle and dihedral parameters during the user mediated atom typing process. With respect, -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 11/4/10 10:09 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" wrote: Sent to CCL by: FyD [fyd : q4md-forcefieldtools.org] Dear Rick Venable, R.E.D. means RESP and ESP charge Derivation. The R.E.D. Tools and R.E.D. Server do not only deal with _RESP_ charges but with _ESP_ charges using various algorithms used in MEP computation. And ESP charges are used in FFs different from AMBER FFs... Then, charge derivation is the first step - charge validation is done in a second step. See http://www.ncbi.nlm.nih.gov/pubmed/20574571 & references cited herein. This is why we wrote "R.E.D. Server is a web service designed to automatically derive RESP and ESP charges, and to build force field libraries for new molecules/molecular fragments. R.E.D. Server provides to computational biologists involved in AMBER, CHARMM, GLYCAM & OPLS force field based biological studies the software and hardware required for charge derivation and force field library building." regards, Francois > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler!=!nhlbi.nih.gov] > Given that RESP/ESP methods are **not** used for the development of > CHARMM force fields (a fragment approach similar to OPLS is used), > the compatibility of molecules with RESP-based charges with the rest > of the CHARMM force fields is somewhat questionable. The use of > other approaches, notably the CHARMM General force field (CGenFF), > is recommended instead of ad hoc web servers for extending the > CHARMM force field to new molecules. > > I did not see anything on the q4md site which discussed this, or > that gave any hints about validation of the molecular descriptions > produced in the context of CHARMM and its distributed force fields.