From owner-chemistry@ccl.net Sat Nov 6 03:58:00 2010 From: "FyD fyd^-^q4md-forcefieldtools.org" To: CCL Subject: CCL: Release of R.E.D. Server 2.0 Message-Id: <-43085-101106035055-21303-irNF9CJ5flXG6+syao41SQ!A!server.ccl.net> X-Original-From: FyD Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Sat, 06 Nov 2010 08:50:48 +0100 MIME-Version: 1.0 Sent to CCL by: FyD [fyd:+:q4md-forcefieldtools.org] Dear Rick, The main idea with the R.E.D. program is to generate a force field (FF) library format (.mol2 file format) with RESP or ESP charge values for new molecules and for potentially any type of molecular fragments (organic, bio-organic & bio-inorganic). Entire Force Field Topology DataBase (FFTopDB) can now be directly generated. These FF libraries are FF atom type independent allowing any user to add the atom types corresponding to the force field of her/his choice. We believe this force field library is convenient because it can be directly displayed in many graphical programs. This FF library can also be converted into a more specific FF library format such as the prep/off/rtf/others? file formats (using a script based approach or a specific program; R.E.DD.B. can handle such scripts/program even for CHARMM). I think this main idea is also summarized (may be in another way) in the back cover of the 12/2010 issue of PCCP: "Methods and computational tools useful for charge derivation and force field topology database building are presented. They give researchers the means to derive rigorously QM MEP-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and/or MD simulations." All is said here. More generally, we selected the references 17-20 in our article taking works from well established groups among others. You can find different references in the literature where ESP charges are used in "CHARMM" (after validation/adjustment or even directly used by users). That being said, I understand some CHARMM developers do not like this idea. Please, Rick, download the R.E.D.-III.4 Tools (it is distributed under the GNU General Public License), use it and tell us what you think should be improved. regards, Francois Quoting "Venable, Richard (NIH/NHLBI) E venabler(a)nhlbi.nih.gov" : > 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. From owner-chemistry@ccl.net Sat Nov 6 12:54:00 2010 From: "elsayed elmeselhy elsayed.elmes.,,.yahoo.com" To: CCL Subject: CCL:G: Antiferromagentism of dinulear transition metal complexes Message-Id: <-43086-101106124929-22329-46SE5f8Q5QZTUXYuIMsitw,,server.ccl.net> X-Original-From: elsayed elmeselhy Content-Type: multipart/alternative; boundary="0-1643125102-1289062161=:531" Date: Sat, 6 Nov 2010 09:49:21 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: elsayed elmeselhy [elsayed.elmes|a|yahoo.com] --0-1643125102-1289062161=:531 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear All Thanks for=A0 Adam Johannes for his useful reply. I have been optimized two= types of dinuclear cobalt complexes with different spin states (singlet, t= riplet, quintet and septet). For one complex, I find the septet state has t= he lowest energy. While for the other complex I found the singlet spin stat= e has the lowest energy. May questions are:=20 (i) should I calculate the singlet broken asymmetry? (ii) What is the recipe to calculate=A0 broken asymmetry? Thanks in advance, Sayed --- On Thu, 11/4/10, Johannes Johansson johjo76*_*gmail.com wrote: > From: Johannes Johansson johjo76*_*gmail.com Subject: CCL:G: Antiferromagentism of dinulear transition metal complexes To: "Mesa, Sayed " Date: Thursday, November 4, 2010, 3:18 PM Dear Sayed, please see the following discussion in the CCL archive:http://www.ccl.net/c= gi-bin/ccl/message-new?2009+07+10+011=0A For further reference:Adam Johannes Johansson, Holger Noack, Per E. M. Sieg= bahn, Genqiang Xue and Lawrence Que Jr.=0A=0ADalton Trans., 2009, 6741-6750 DOI:=A010.1039/B907263B =0ABest regards / Johannes =0A--=A0 =0AAdam Johannes Johansson Ph.D., M.Sc. Division of Physical Chemistry KTH (Royal Institute of Technology) Teknikringen 36 SE-100 44 Stockholm Sweden Office: 087908217 =0A =0A 2010/11/2 Sayed Mesa elsayed.elmes-,-yahoo.com =0A =0ASent to CCL by: "Sayed =A0Mesa" [elsayed.elmes##yahoo.com] =0A =0ADear All: =0A =0AI have measured the magnetism of some dinulear transition metal complexe= s, where transition metals are Co2+, Ni2+ & Cu2+. Some complexes shows stro= ng antiferromagentism and some others shows weak antiferromagentism while t= he remaining are ferromagentic. =0A=0A =0AI would like to optimize the geometries of these complexes with DFT (Gau= ssian), but I am confused how can I define the spin of the dinuclear comple= xs. By the way, the total number of eletrons of complexes is even in all ca= ses. =0A=0A =0AI 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 st= ate may have 1 or 3. =0AMy question: Should I optimize the geometries of all probabilities of sp= in states and then choose the lowest energy among them. This scenario is va= lid? =0A =0AThanks in advance, =0ASayed =0A =0A =0A =0A-=3D This is automatically added to each message by the mailing script = =3D- =0A =0AE-mail to subscribers: CHEMISTRY[-]ccl.net or use: =0A =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message =0A =0AE-mail to administrators: CHEMISTRY-REQUEST[-]ccl.net or use =0A =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message =0A =0A=0A =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml =0A =0A=0A =0A=0A=0A =0A=0A =0A =A0 =A0 =A0http://www.ccl.net/spammers.txt =0A =0A=0A =0A =0A =0A=0A=0A=0A --0-1643125102-1289062161=:531 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear All

Thanks for  Adam Johannes for his use= ful reply. I have been optimized two types of dinuclear cobalt complexes wi= th different spin states (singlet, triplet, quintet and septet). For one co= mplex, I find the septet state has the lowest energy. While for the other c= omplex I found the singlet spin state has the lowest energy. May questions = are:

(i) should I calculate the singlet broken asymmetry?
(ii) What is the recip= e to calculate  broken asymmetry?

Thanks in advance,
Sayed
--- On Thu, 11/4/10, Johannes Johansson johjo76*_*gmail.com <own= er-chemistry..ccl.net> wrote:

Fro= m: Johannes Johansson johjo76*_*gmail.com <owner-chemistry..ccl.net>Subject: CCL:G: Antiferromagentism of dinulear transition metal complexes=
To: "Mesa, Sayed " <elsayed.elmes..yahoo.com>
Date: Thu= rsday, November 4, 2010, 3:18 PM

Dear Sayed,
=
please see the following discussion in the CCL archive:=0A

For further reference:
Adam Johannes Johansson, Holger Noack, Per E. M. Si= egbahn, Genqiang Xue and Lawrence Que Jr.
=0A
=0ADalton Trans., 2009, 6741-6750

DOI: 10.1039/B907263B=
=0ABes= t regards / Johannes
=0A-- =0AAdam Johannes Johansson
Ph.D., M.Sc.
Division of Physical Chemist= ry
KTH (Royal Institute of Technology)
Teknikringen 36
SE-100 44 S= tockholm
Sweden
Office: 087908217

=0A

=0A
<= /span>

2010/11/2 Sayed Mesa= elsayed.elmes-,-yahoo.com <owner-chemistry[-]ccl.net>
=0A<= blockquote class=3D"yiv579133822gmail_quote" style=3D"margin: 0pt 0pt 0pt 0= .8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
= =0ASent to CCL by: "Sayed  Mesa" [elsayed.elmes##yahoo.com]
=0A
=0ADear= All:
=0A
=0AI have measured the magnetism of some dinulear transitio= n metal complexes, where transition metals are Co2+, Ni2+ & Cu2+. Some = complexes shows strong antiferromagentism and some others shows weak antife= rromagentism while the remaining are ferromagentic.
=0A=0A
=0AI would= like to optimize the geometries of these complexes with DFT (Gaussian), bu= t 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.
= =0A=0A
=0AI know that diCobalet complex may have spin state of 1, 3, 5 o= r 7, while diNikel complex have have spin states 1, 3 or 5. For dicopper, t= he spin state may have 1 or 3.
=0AMy question: Should I optimize the geo= metries of all probabilities of spin states and then choose the lowest ener= gy among them. This scenario is valid?
=0A
=0AThanks in advance,
= =0ASayed
=0A
=0A
=0A
=0A-=3D This is automatically added to eac= h message by the mailing script =3D-
=0A
=0AE-mail to subscribers: CHEMISTRY[-]ccl.net or us= e:
=0A      http://www.ccl.net/cgi-bi= n/ccl/send_ccl_message
=0A
=0AE-mail to administrators: CHEMISTRY-REQUEST[-]= ccl.net or use
=0A      http://ww= w.ccl.net/cgi-bin/ccl/send_ccl_message
=0A
=0ASubscribe/Unsubscri= be:
=0A      http://www.ccl.net/chemis= try/sub_unsub.shtml
=0A
=0ABefore posting, check wait time at: http://www.= ccl.net
=0A
=0AJob: http://www.ccl.net/jobs
=0AConferences: http://server.ccl.net/chemistry/announcements/= conferences/
=0A
=0ASearch Messages: htt= p://www.ccl.net/chemistry/searchccl/index.shtml
=0A
=0A   &n= bsp;  http://www.ccl.net/spammers.txt
=0A
=0ARTFI: http://www.ccl.net/chemistry/aboutccl/instructions/<= br>=0A
=0A
=0A




=0A

=0A=0A --0-1643125102-1289062161=:531-- From owner-chemistry@ccl.net Sat Nov 6 14:45:00 2010 From: "John McKelvey jmmckel[A]gmail.com" To: CCL Subject: CCL: LAPACK, BLAS Message-Id: <-43087-101106144354-23137-rUz/hNIDMLPB9Cr1W0poBg#,#server.ccl.net> X-Original-From: John McKelvey Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 6 Nov 2010 14:43:47 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel{:}gmail.com] Folks, I've found that the free WINDOS G95 compiler is quite useful. Are there LAPACK and BLAS libraries that would link with Windows G95 object files? Many thanks! John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel#,#gmail.com From owner-chemistry@ccl.net Sat Nov 6 17:19:01 2010 From: "Jean Jules FIFEN julesfifen(-)gmail.com" To: CCL Subject: CCL:G: Antiferromagentism of dinulear transition metal complexes Message-Id: <-43088-101106052816-26777-Pe1f1CwbacbqxiJyirWugg . server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: multipart/alternative; boundary=0015175cb2fc739c1d04945f02e9 Date: Sat, 6 Nov 2010 10:28:10 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen%a%gmail.com] --0015175cb2fc739c1d04945f02e9 Content-Type: text/plain; charset=ISO-8859-1 Yes, you can do such computations. 1. It will be easy to you for doing it by using a software viewer as gaussview 5.0. From there, you can specify the spin of individual group(s) of atoms using the atom group editor. For more precisions, you can read the page 27 of the manual of this software. After specifying the spin multiplicities and charges, you have now to add the usual key word *opt freq* to do the optimization and frequency calculation. 2. Another way to do it is, to built the input file as it is done to do BSSE computations; but remove the key word BSSE. For such method, see gaussian03 manual. Best regards, Jules. On 2 November 2010 20:49, Sayed Mesa elsayed.elmes++yahoo.com < owner-chemistry]=[ccl.net> wrote: > > 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> > > -- Jean Jules FIFEN, +237 75 21 61 39 +237 94 67 65 05 University of Ngaoundere, PO.BOX 454 Ngaoundere --0015175cb2fc739c1d04945f02e9 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Yes, you can do such computations.
  1. It will be e= asy to you for doing it by using a software viewer as gaussview 5.0. From t= here, you can specify the spin of individual group(s) of atoms using the at= om group editor. For more precisions, you can read the page 27 of the manua= l of this software. After specifying the spin multiplicities and charges, y= ou have now to add the usual key word opt freq to do the optimizatio= n and frequency calculation.
  2. Another way to do it is, to built the input file as it is done to do BS= SE computations; but remove the key word BSSE. For such method, see gaussia= n03 manual.
Best regards,

Jules.


On 2 November 2010 20:49, Sayed Mesa elsayed.elmes++yahoo.com <owner-chemistry]=[ccl.net&g= t; wrote:

Sent to CCL by: "Sayed =A0Mesa" [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 str= ong antiferromagentism and some others shows weak antiferromagentism while = the remaining are ferromagentic.

I would like to optimize the geometries of these complexes with DFT (Gaussi= an), 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 di= Nikel 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



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY]=[ccl.net or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST]=[ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/





--
Jean Jules FIFEN,
+2= 37 75 21 61 39
+237 94 67 65 05
University of Ngaoundere,
PO.BOX 4= 54 Ngaoundere
--0015175cb2fc739c1d04945f02e9-- From owner-chemistry@ccl.net Sat Nov 6 17:54:01 2010 From: "Phil Hasnip pjh503-*-york.ac.uk" To: CCL Subject: CCL: LAPACK, BLAS Message-Id: <-43089-101106173922-19707-sPFEEi2AzN259x+gsXAKzg#%#server.ccl.net> X-Original-From: Phil Hasnip Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Date: 06 Nov 2010 21:39:08 +0000 Mime-Version: 1.0 Sent to CCL by: Phil Hasnip [pjh503*o*york.ac.uk] Dear John, >I've found that the free WINDOS G95 compiler is quite useful. Are >there LAPACK and BLAS libraries that would link with Windows G95 >object files? If you don't care about speed you could download and compile the reference implementation from netlib. Alternatively I find the fastest BLAS to be GotoBLAS, so you could download that from the University of Texas site and try to compile that with g95 under Windows (NB GotoBLAS2 won't work on the i7 series though). Yours, Phil Hasnip ------------------------------------------------------- Dr Phil Hasnip Email: pjh503\a/york.ac.uk Dept of Physics University of York Tel: +44 (0)1904 434624 York YO10 5DD