From owner-chemistry@ccl.net Wed Jul 18 02:51:00 2012 From: "uekstrom ~~ gmail.com uekstrom ~~ gmail.com" To: CCL Subject: CCL: Latest issue of Foundations of Chemistry Message-Id: <-47219-120718024622-10747-ZZUaOR/37qPlcRLMojZ5sg^-^server.ccl.net> X-Original-From: "uekstrom#,#gmail.com" Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 18 Jul 2012 08:46:16 +0200 MIME-Version: 1.0 Sent to CCL by: "uekstrom]_[gmail.com" [uekstrom]_[gmail.com] Dear Tom, I did not mean that no subscriber to CCL is interested in Frontiers of Chemistry. What I meant was that Eric Scerri could use one or two sentences in his posts to write _why_ CCL subscribers should check out his blog posts or journal issues. You may note that he has not replied (on CCL at least) to any of the people discussing his blog posts. On is tempted to think that he just posts them here to get more readers, and is not really interested in discussion about computational chemistry. Regards, Ulf Ekstrom, University of Oslo From owner-chemistry@ccl.net Wed Jul 18 03:25:00 2012 From: "Hyunbok Lee mutebeat*|*gmail.com" To: CCL Subject: CCL: GaussView Error : CConnectionGFCHK::ParseGFCHK() Message-Id: <-47220-120718025010-10946-50i9TPnimS6dO33TYRjcxg:_:server.ccl.net> X-Original-From: Hyunbok Lee Content-Type: multipart/alternative; boundary=000e0cdfdb529801fc04c515126f Date: Wed, 18 Jul 2012 15:50:03 +0900 MIME-Version: 1.0 Sent to CCL by: Hyunbok Lee [mutebeat-,-gmail.com] --000e0cdfdb529801fc04c515126f Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Javier, I did as you commented, and the I can open the fch file ! I sincerely appreciate your kind response. I'm sorry but could you tell me about what is the difference between "basis functions" and "independent basis functions" ? Best regards, Hyunbok Lee On Tue, Jul 17, 2012 at 6:24 PM, Javier Cerezo jcb1-*-um.es < owner-chemistry%%ccl.net> wrote: > > Sent to CCL by: Javier Cerezo [jcb1- -um.es] > It seems to be a bug in your gv version (I also have the same problem). > The workaround I'm using is: > > 1) Convert your chk in fchk: formchk yourfile.chk > > 2) Inspect the fchk file. Near the header you have info about number of > basis set. The problem (at least in my case) arises when "Number of basis > functions" is not the same as "Number of independent basis functions". To > make it work you need to edit the file making Number of basis > functions=3DNumber of independent basis functions. > > The edited fchk file should be opened with no problems by gv. > > Javier > > > El 17/07/12 09:48, Hyunbok Lee mutebeat!^!gmail.com escribi=F3: > > Sent to CCL by: "Hyunbok Lee" [mutebeat||gmail.com] >> Deal all, >> >> I opened chk file on GaussView, but it showed following error message: >> >> CConnectionGFCHK::Parse_GFCHK(**) >> Missing or bad data: Alpha Ortbial Energies >> Line Number 1737 >> >> I think the calculation is done without a problem. >> What is the problem? and what is the meaning of this error message? >> Any advise will be appreciated. >> >> Thanks in advance. >> >> Hyunbok Lee> >> >> > > > -- > Javier CEREZO BASTIDA > PhD Student > Physical Chemistry > Universidad de Murcia > Murcia (Spain) > Tel: (+34)868887434 > > > > > -=3D This is automatically added to each message by the mailing script = =3D-> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message http://www.ccl.net/cgi-bin/**ccl/send_ccl_message chemistry/announcements/**conferences/ > > Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml http://www.ccl.net/spammers.**txt > > RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/ > > > --000e0cdfdb529801fc04c515126f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Javier,


I did as you commented, and = the I can open the fch file !
I sincerely appreciate your kind re= sponse.

I'm sorry but could you tell me about = what is the difference between
"basis functions" and "independent basis functions" ?


Best regards,

Hyunbok Lee


On Tue, Jul 17,= 2012 at 6:24 PM, Javier Cerezo jcb1-*-um.es <= span dir=3D"ltr"><owner-chemistry%%ccl.net> wrote:

Sent to CCL by: Javier Cerezo [jcb1- -um.es]
It seems to be a bug in your gv version (I also have the same problem). The= workaround I'm using is:

1) Convert your chk in fchk: formchk yourfile.chk

2) Inspect the fchk file. Near the header you have info about number of bas= is set. The problem (at least in my case) arises when "Number of basis= functions" is not the same as "Number of independent basis funct= ions". To make it work you need to edit the file making Number of basi= s functions=3DNumber of independent basis functions.

The edited fchk file should be opened with no problems by gv.

Javier


El 17/07/12 09:48, Hyunbok Lee mutebeat!^!gmail.com escribi=F3:

Sent to CCL by: "Hyunbok =A0Lee" [mutebeat||gmail.com]
Deal all,

I opened chk file on GaussView, but it showed following error message:

CConnectionGFCHK::Parse_GFCHK()
Missing or bad data: Alpha Ortbial Energies
Line Number 1737

I think the calculation is done without a problem.
What is the problem? and what is the meaning of this error message?
Any advise will be appreciated.

Thanks in advance.

Hyunbok Lee>




--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434



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--000e0cdfdb529801fc04c515126f-- From owner-chemistry@ccl.net Wed Jul 18 09:41:01 2012 From: "G. Gopakumar gopakumar.gopinadhan_._gmail.com" To: CCL Subject: CCL: Latest issue of Foundations of Chemistry Message-Id: <-47221-120718020852-9499-RqaXVAH7qzpJaWbBFc/Wrg%a%server.ccl.net> X-Original-From: "G. Gopakumar" Content-Type: multipart/alternative; boundary=e89a8f642902e1ad9d04c5147e55 Date: Wed, 18 Jul 2012 08:08:25 +0200 MIME-Version: 1.0 Sent to CCL by: "G. Gopakumar" [gopakumar.gopinadhan++gmail.com] --e89a8f642902e1ad9d04c5147e55 Content-Type: text/plain; charset=ISO-8859-1 Dear Ulf, I hope there was a misunderstanding. "Foundations of Chemistry" is the official journal of "International Society for the Philosophy of Chemistry (ISPC)" and Eric's e-mail was to remind readers about the latest issue of the same. I hope it fits to the general interest of CCL. with kind regards Gopakumar * * On 17 July 2012 09:05, uekstrom+/-gmail.com uekstrom+/-gmail.com < owner-chemistry##ccl.net> wrote: > > Sent to CCL by: "uekstrom]|[gmail.com" [uekstrom]|[gmail.com] > >On Tue, Jul 17, 2012 at 12:40 AM, Eric Scerri scerri:+:chem.ucla.edu ccl.net> wrote: > > > > > >Foundations of Chemistry, Volume 14, Number 2 / July 2012 > > > >http://www.springerlink.com/content/1386-4238/14/2/ > > [..] > > Seriously? Can you at least make your posts mildly relevant to the CCL > list? Aren't you past the point of desperate self promotion by > spamming? > > Cheers, > Ulf Ekstrom, University of Oslo> > > --e89a8f642902e1ad9d04c5147e55 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Ulf,

=A0=A0=A0=A0 I hope there was a misunderstanding.

= "Foundations of Chemistry"=A0 is the official journal of "In= ternational Society
for the Philosophy of Chemistry (ISPC)" and Er= ic's e-mail was to remind
readers about the latest issue of the same. I hope it fits to the general <= br>interest of CCL.

with kind regards

Gopakumar=A0

=A0
On 17 July 2012 09:05, uekstrom+/-gmail.com uekstrom+/-gmail.com <owner-chemistry##ccl.n= et> wrote:

Sent to CCL by: "uekstrom]|[gmail.com" [uekstrom]|[gmail.com]
>On Tue, Jul 17, 2012 at 12:40 AM, Eric Scerri scerri:+:chem.ucla.edu <owner-chemistry/./= ccl.net> wrote:
>
>
>Foundations of Chemistry, =A0Volume 14, Number 2 / July 2012
>
>http://www.springerlink.com/content/1386-4238/14/2/

[..]

Seriously? Can you at least make your posts mildly relevant to the CCL
list? Aren't you past the point of desperate self promotion by
spamming?

Cheers,
Ulf Ekstrom, University of Oslo



-=3D This is automatically added to each message by the mailing script =3D-=
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--e89a8f642902e1ad9d04c5147e55-- From owner-chemistry@ccl.net Wed Jul 18 10:16:00 2012 From: "Andras Borosy andras.borosy[*]givaudan.com" To: CCL Subject: CCL: Latest issue of Foundations of Chemistry Message-Id: <-47222-120718034843-9971-F+s3LVYvjXLYJJlzftUXhA ~ server.ccl.net> X-Original-From: Andras Borosy Content-Type: multipart/alternative; boundary="=_alternative 002ADE9BC1257A3F_=" Date: Wed, 18 Jul 2012 09:48:21 +0200 MIME-Version: 1.0 Sent to CCL by: Andras Borosy [andras.borosy/a\givaudan.com] This is a multipart message in MIME format. --=_alternative 002ADE9BC1257A3F_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Colleagues, I do agree with Mr. Ekstrom. Best wishes, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com > From: "uekstrom ~~ gmail.com uekstrom ~~ gmail.com"=20 To: "Borosy, Andras " Date: 18.07.2012 09:45 Subject: CCL: Latest issue of Foundations of Chemistry Sent by: owner-chemistry+andras.borosy=3D=3Dgivaudan.com-x-ccl.net Sent to CCL by: "uekstrom]=5F[gmail.com" [uekstrom]=5F[gmail.com] Dear Tom, I did not mean that no subscriber to CCL is interested in Frontiers of Chemistry. What I meant was that Eric Scerri could use one or two sentences in his posts to write =5Fwhy=5F CCL subscribers should check out his blog posts or journal issues. You may note that he has not replied (on CCL at least) to any of the people discussing his blog posts. On is tempted to think that he just posts them here to get more readers, and is not really interested in discussion about computational chemistry. Regards, Ulf Ekstrom, University of Oslo -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessagehttp://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage Subscribe/Unsubscribe:=20 http://www.ccl.net/chemistry/sub=5Funsub.shtmlJob: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--=_alternative 002ADE9BC1257A3F_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Colleagues,

I do agree with Mr. Ekstrom.

Best wishes,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert

Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  htt= p://www.givaudan.com



From:     =    "uekstrom ~~ gmail.com uekstrom ~~ gmail.com" <owner-chemistry-x-ccl.net>
To:     &n= bsp;  "Borosy, Andras " <andras.borosy-x-givaudan.com>
Date:     =    18.07.2012 09:45
Subject:   &nbs= p;    CCL: Latest issue of Foundations of Chemistry
Sent by:   &nbs= p;    owner-chemistry+andr= as.borosy=3D=3Dgivaudan.com-x-ccl.net




Sent to CCL by: "uekstrom]=5F[gmail.com" [uekstrom]=5F[gmail.com]=
Dear Tom,
I did not mean that no subscriber to CCL is interested in Frontiers of
Chemistry. What I meant was that Eric Scerri could use one or two
sentences in his posts to write =5Fwhy=5F CCL subscribers should check out<= br> his blog posts or journal issues. You may note that he has not replied
(on CCL at least) to any of the people discussing his blog posts. On
is tempted to think that he just posts them here to get more readers,
and is not really interested in discussion about computational
chemistry.

Regards,
Ulf Ekstrom, University of Oslo



-=3D This is automatically added to each message by the mailing script =3D-=      http://www.ccl.net/cgi-bin/ccl/sen= d=5Fccl=5Fmessage
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     http://www.ccl.net/chemistry/sub=5Funsub.= shtml

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

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--=_alternative 002ADE9BC1257A3F_=-- From owner-chemistry@ccl.net Wed Jul 18 10:51:00 2012 From: "Javier Cerezo jcb1]=[um.es" To: CCL Subject: CCL:G: GaussView Error : CConnectionGFCHK::ParseGFCHK() Message-Id: <-47223-120718043300-3746-B9HR9S+tY8wR3+LVB2WjbA-,-server.ccl.net> X-Original-From: Javier Cerezo Content-Type: multipart/alternative; boundary="------------070302030304020202000408" Date: Wed, 18 Jul 2012 10:32:53 +0200 MIME-Version: 1.0 Sent to CCL by: Javier Cerezo [jcb1..um.es] This is a multi-part message in MIME format. --------------070302030304020202000408 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Hi Hyunbok Lee, I don't exactly know the difference, I guess that it should be related to the fact that in some cases the whole set of basis functions are not independent (i.e. some of them are just a linear combination of the rest). Therefore, gaussian makes the distinction between the total number of basis functions ("basis functions") and the number of those linearly independent ("independent basis functions"). Normally, I have the same number in both sets (i.e. all basis functions are linearly independent). Obviously, when there is a difference, both sets will give rise to the same results so the smaller one ("independent basis functions") is taken for computational efficiency. The problem seem to strive in how gaussview gets the number of functions to be read, as it apparently get it from "Number of basis functions" while in the chk file the information refers to the independent set. For example, in your case, if you go to Line Number 1737, as the error says, you'll see the number of Alpha Orbital Energies equals the "Number of independent basis functions" (recall that within the Rothaan-Hall approach, one obtains the same number of molecular orbitals as basis functions where used) not the "Number of basis functions". As the program was expecting a larger number of orbital energies than the actual one, it sorts out that error. Well, this is just my appreciation (so error-prone) and still did not answer why one can get such linear dependencies in the basis set. But hope it gives you an idea to start with. Javier El 18/07/12 08:50, Hyunbok Lee mutebeat*|*gmail.com escribió: > Dear Javier, > > > I did as you commented, and the I can open the fch file ! > I sincerely appreciate your kind response. > > I'm sorry but could you tell me about what is the difference between > "basis functions" and "independent basis functions" ? > > > Best regards, > > Hyunbok Lee > > > On Tue, Jul 17, 2012 at 6:24 PM, Javier Cerezo jcb1-*-um.es > > wrote: > > > Sent to CCL by: Javier Cerezo [jcb1- -um.es ] > It seems to be a bug in your gv version (I also have the same > problem). The workaround I'm using is: > > 1) Convert your chk in fchk: formchk yourfile.chk > > 2) Inspect the fchk file. Near the header you have info about > number of basis set. The problem (at least in my case) arises when > "Number of basis functions" is not the same as "Number of > independent basis functions". To make it work you need to edit the > file making Number of basis functions=Number of independent basis > functions. > > The edited fchk file should be opened with no problems by gv. > > Javier > > > El 17/07/12 09:48, Hyunbok Lee mutebeat!^!gmail.com > escribió: > > Sent to CCL by: "Hyunbok Lee" [mutebeat||gmail.com > ] > Deal all, > > I opened chk file on GaussView, but it showed following error > message: > > CConnectionGFCHK::Parse_GFCHK() > Missing or bad data: Alpha Ortbial Energies > Line Number 1737 > > I think the calculation is done without a problem. > What is the problem? and what is the meaning of this error > message? > Any advise will be appreciated. > > Thanks in advance. > > Hyunbok Lee> > > > > > -- > Javier CEREZO BASTIDA > PhD Student > Physical Chemistry > Universidad de Murcia > Murcia (Spain) > Tel: (+34)868887434 > > > > > -= This is automatically added to each message by the mailing > script =- > E-mail to subscribers: CHEMISTRY[a]ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST[a]ccl.net > or useConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- Javier CEREZO BASTIDA PhD Student Physical Chemistry Universidad de Murcia Murcia (Spain) Tel: (+34)868887434 --------------070302030304020202000408 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Hyunbok Lee,

I don't exactly know the difference, I guess that it should be related to the fact that in some cases the whole set of basis functions are not independent (i.e. some of them are just a linear combination of the rest). Therefore, gaussian makes the distinction between the total number of basis functions ("basis functions") and the number of those linearly independent ("independent basis functions"). Normally, I have the same number in both sets (i.e. all basis functions are linearly independent). Obviously, when there is a difference, both sets will give rise to the same results so the smaller one ("independent basis functions") is taken for computational efficiency.

The problem seem to strive in how gaussview gets the number of functions to be read, as it apparently get it from "Number of basis functions" while in the chk file the information refers to the independent set. For example, in your case, if you go to Line Number 1737, as the error says, you'll see the number of Alpha Orbital Energies equals the "Number of independent basis functions" (recall that within the Rothaan-Hall approach, one obtains the same number of molecular orbitals as basis functions where used) not the "Number of basis functions". As the program was expecting a larger number of orbital energies than the actual one, it sorts out that error.

Well, this is just my appreciation (so error-prone) and still did not answer why one can get such linear dependencies in the basis set. But hope it gives you an idea to start with.

Javier

El 18/07/12 08:50, Hyunbok Lee mutebeat*|*gmail.com escribió:
Dear Javier,


I did as you commented, and the I can open the fch file !
I sincerely appreciate your kind response.

I'm sorry but could you tell me about what is the difference between
"basis functions" and "independent basis functions" ?


Best regards,

Hyunbok Lee


On Tue, Jul 17, 2012 at 6:24 PM, Javier Cerezo jcb1-*-um.es <owner-chemistry[a]ccl.net> wrote:

Sent to CCL by: Javier Cerezo [jcb1- -um.es]
It seems to be a bug in your gv version (I also have the same problem). The workaround I'm using is:

1) Convert your chk in fchk: formchk yourfile.chk

2) Inspect the fchk file. Near the header you have info about number of basis set. The problem (at least in my case) arises when "Number of basis functions" is not the same as "Number of independent basis functions". To make it work you need to edit the file making Number of basis functions=Number of independent basis functions.

The edited fchk file should be opened with no problems by gv.

Javier


El 17/07/12 09:48, Hyunbok Lee mutebeat!^!gmail.com escribió:

Sent to CCL by: "Hyunbok  Lee" [mutebeat||gmail.com]
Deal all,

I opened chk file on GaussView, but it showed following error message:

CConnectionGFCHK::Parse_GFCHK()
Missing or bad data: Alpha Ortbial Energies
Line Number 1737

I think the calculation is done without a problem.
What is the problem? and what is the meaning of this error message?
Any advise will be appreciated.

Thanks in advance.

Hyunbok Lee>




--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434




E-mail to subscribers: CHEMISTRY[a]ccl.net or use:
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST[a]ccl.net or use
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
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Before posting, check wait time at: http://www.ccl.net

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--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
--------------070302030304020202000408-- From owner-chemistry@ccl.net Wed Jul 18 11:26:00 2012 From: "Hao-Bo Guo guohaobo++gmail.com" To: CCL Subject: CCL: Latest issue of Foundations of Chemistry Message-Id: <-47224-120718094341-19400-IT5yU+aQlyxYptlx98PlNA|-|server.ccl.net> X-Original-From: Hao-Bo Guo Content-Type: multipart/alternative; boundary=20cf3079bdda3b5fe304c51ad989 Date: Wed, 18 Jul 2012 09:43:31 -0400 MIME-Version: 1.0 Sent to CCL by: Hao-Bo Guo [guohaobo() gmail.com] --20cf3079bdda3b5fe304c51ad989 Content-Type: text/plain; charset=ISO-8859-1 Dear Ulf Ekstrom, I read Dr. Eric Scerri's posts and his blog from CCL and do feel some of them are interesting. I agree with you that CCL subscribers are mostly computational chemists or physicists, but that doesn't mean that we do not need to have a deeper thought of the fundamental chemistry and physics. Besides, everyone is going to enjoy his/her publications being cited or being interested, and therefore you should not criticize the willingness of any authors, including bloggers, for getting more readers. Regards, Hao-Bo Guo, Oak Ridge National Laboratory. On Wed, Jul 18, 2012 at 2:46 AM, uekstrom ~~ gmail.com uekstrom ~~ gmail.com wrote: > > Sent to CCL by: "uekstrom]_[gmail.com" [uekstrom]_[gmail.com] > Dear Tom, > I did not mean that no subscriber to CCL is interested in Frontiers of > Chemistry. What I meant was that Eric Scerri could use one or two > sentences in his posts to write _why_ CCL subscribers should check out > his blog posts or journal issues. You may note that he has not replied > (on CCL at least) to any of the people discussing his blog posts. On > is tempted to think that he just posts them here to get more readers, > and is not really interested in discussion about computational > chemistry. > > Regards, > Ulf Ekstrom, University of Oslo> > > --20cf3079bdda3b5fe304c51ad989 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Ulf Ekstrom,
I read Dr. Eric Scerri's posts and his blog from C= CL and do feel some of them are interesting.
I agree with you that CCL s= ubscribers are mostly computational chemists or physicists, but that doesn&= #39;t mean that we do not need to have a deeper thought of the fundamental = chemistry and physics. Besides, everyone is going to enjoy his/her publicat= ions being cited or being interested, and therefore you should not criticiz= e the willingness of any authors, including bloggers, for getting more read= ers.
Regards,
Hao-Bo Guo, Oak Ridge National Laboratory.

On Wed, Jul 18, 2012 at 2:46 AM, uekstrom ~~ gmail.com uekstrom ~~ gmail.c= om <owner-chemistry*|*ccl.net> wrote:

Sent to CCL by: "uekstrom]_[gmail.com" [uekstrom]_[gmail.com]
Dear Tom,
I did not mean that no subscriber to CCL is interested in Frontiers of
Chemistry. What I meant was that Eric Scerri could use one or two
sentences in his posts to write _why_ CCL subscribers should check out
his blog posts or journal issues. You may note that he has not replied
(on CCL at least) to any of the people discussing his blog posts. On
is tempted to think that he just posts them here to get more readers,
and is not really interested in discussion about computational
chemistry.

Regards,
Ulf Ekstrom, University of Oslo



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY*|*ccl.n= et or use:
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--20cf3079bdda3b5fe304c51ad989-- From owner-chemistry@ccl.net Wed Jul 18 12:00:00 2012 From: "Ramon Crehuet rcsqtc!=!iqac.csic.es" To: CCL Subject: CCL: Latest issue of Foundations of Chemistry Message-Id: <-47225-120718115402-16459-SE5vIe2fZTIwunGaKuFXgA * server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=ISO-8859-1 Date: Wed, 18 Jul 2012 17:54:03 +0200 MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet [rcsqtc(a)iqac.csic.es]
Dear CCLers,
I don't think we should discuss whether the articles in "The foundations of Chemistry" are interesting to CCL readers. I am sure there are many articles in J. Comput. Chem. or J. Chem. Theor. Comput. interesting to CCL readers. Do we expect the ACS or Wiley to start posting the table of contents for each new issue? Considering the vast number of journals that can be interesting to us, I do not think this is what CCLers would prefer.

There are better channels to get the newest publications in an area, such as getting e-mail alerts. Or, in the case of the Foundations of Chemistry, subscribing to the page via RSS. This is a much more selective way to distribute the contents.

Regards,

Ramon Crehuet


On 18/07/12 15:43, Hao-Bo Guo guohaobo++gmail.com wrote:
Dear Ulf Ekstrom,
I read Dr. Eric Scerri's posts and his blog from CCL and do feel some of them are interesting.
I agree with you that CCL subscribers are mostly computational chemists or physicists, but that doesn't mean that we do not need to have a deeper thought of the fundamental chemistry and physics. Besides, everyone is going to enjoy his/her publications being cited or being interested, and therefore you should not criticize the willingness of any authors, including bloggers, for getting more readers.
Regards,
Hao-Bo Guo, Oak Ridge National Laboratory.

On Wed, Jul 18, 2012 at 2:46 AM, uekstrom ~~ gmail.com uekstrom ~~ gmail.com <owner-chemistry*|*ccl.net> wrote:

Sent to CCL by: "uekstrom]_[gmail.com" [uekstrom]_[gmail.com]
Dear Tom,
I did not mean that no subscriber to CCL is interested in Frontiers of
Chemistry. What I meant was that Eric Scerri could use one or two
sentences in his posts to write _why_ CCL subscribers should check out
his blog posts or journal issues. You may note that he has not replied
(on CCL at least) to any of the people discussing his blog posts. On
is tempted to think that he just posts them here to get more readers,
and is not really interested in discussion about computational
chemistry.

Regards,
Ulf Ekstrom, University of Oslo



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-- 
**************************************************************
Ramon Crehuet, PhD
Tenured researcher (Cientific titular)
Institute of Advanced Chemistry of Catalunya
http://www.iqac.csic.es/qteor
https://twitter.com/rcrehuet
IQAC - CSIC
Tel. +34 934006116
Jordi Girona 18-26
08034 Barcelona (Spain)
**************************************************************
From owner-chemistry@ccl.net Wed Jul 18 13:18:01 2012 From: "uekstrom*|*gmail.com uekstrom*|*gmail.com" To: CCL Subject: CCL: Latest issue of Foundations of Chemistry Message-Id: <-47226-120718131628-14510-Dg3LNOHK+IFLRCrSp3G7HQ-,-server.ccl.net> X-Original-From: "uekstrom^^^gmail.com" Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 18 Jul 2012 19:16:19 +0200 MIME-Version: 1.0 Sent to CCL by: "uekstrom!^!gmail.com" [uekstrom!^!gmail.com] I would like to apologize for criticizing Eric Scerri's posts to the CCL using unfortunate language. I still don't think it is reasonable to just post links to new journal issues or blog posts to a discussion forum without making any effort to explain in the advertisements why they fit with the topic of the forum. I have read all the three blog posts that Eric Scerri advertised recently on the CCL list, and I do not understand how they relate to research in computational chemistry. In these blog posts Scerri takes a very phenomenological approach to chemistry teaching, and barely even mentions the extremely important fact that the questions he discusses can be addressed computationally. It was not my intention to play moderator, sorry about that. Regards, Ulf Ekstrom, University of Oslo From owner-chemistry@ccl.net Wed Jul 18 13:52:00 2012 From: "may abdelghani may01dz[*]yahoo.fr" To: CCL Subject: CCL: positive energy of the frontier orbital Message-Id: <-47227-120718134257-25049-3LXKy+swEPI/4NpqR8+LFQ+/-server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="-888064777-576117938-1342633368=:95199" Date: Wed, 18 Jul 2012 18:42:48 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz.:.yahoo.fr] ---888064777-576117938-1342633368=:95199 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable =0A=0ADear CCL'ers If=A0 the frontier orbital=0A(HOMO's) energy of a compound have a positive = value, is this a conclusive evidence=0Athat this compound is a unstable=0Ao= ne. A.May =0A=0A ---888064777-576117938-1342633368=:95199 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A=0A<= p class=3D"MsoNormal" dir=3D"LTR" style=3D"text-align: left; direction: ltr= ; unicode-bidi: embed;">De= ar CCL'ers

If  the frontier orbital=0A(HOMO's) ene= rgy of a compound have a positive value, is this a conclusive evidenc= e=0Athat this compound is a unstable=0Aone.


A.May

=0A=0A
---888064777-576117938-1342633368=:95199-- From owner-chemistry@ccl.net Wed Jul 18 15:02:01 2012 From: "John Keller jwkeller!A!alaska.edu" To: CCL Subject: CCL: positive energy of the frontier orbital Message-Id: <-47228-120718145755-14103-+ybpW+XdPKBbkNKIEMN4BA||server.ccl.net> X-Original-From: John Keller Content-Type: multipart/alternative; boundary=20cf307c9fbc3a80fd04c51f3d82 Date: Wed, 18 Jul 2012 10:57:48 -0800 MIME-Version: 1.0 Sent to CCL by: John Keller [jwkeller!A!alaska.edu] --20cf307c9fbc3a80fd04c51f3d82 Content-Type: text/plain; charset=ISO-8859-1 Dear Adbelghani, A positive value for the HOMO just means those electrons are rather loosely bound in the ion or molecule, as you might find in various organic anions. The main criterion for stability (at a given level of theory) is whether the molecule or ion optimizes to a stable minimum value, and frequency analysis shows no imaginary (negative) vibrational modes. Of course on this basis, tetrahedrane and many other molecules are "stable". So the practical aspects of stability must be ascertained by comparison with similar molecules, and analysis of the activation barriers for isomerization into more stable isomers. John Keller On Wed, Jul 18, 2012 at 9:42 AM, may abdelghani may01dz[*]yahoo.fr < owner-chemistry\a/ccl.net> wrote: > Dear CCL'ers > > If the frontier orbital (HOMO's) energy of a compound have a positive > value, is this a conclusive evidence that this compound is a unstable one. > > > A.May > --20cf307c9fbc3a80fd04c51f3d82 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Adbelghani,
A positive value for the HOMO just means th= ose electrons are rather loosely bound in the ion or molecule, as you might= find in various organic anions. The main criterion for stability (at a giv= en level of theory) =A0is whether the molecule or ion optimizes to a stable= minimum value, and frequency analysis shows no imaginary (negative) vibrat= ional modes. Of course on this basis, tetrahedrane and many other molecules= are "stable". So the practical aspects of stability must be asce= rtained by comparison with similar molecules, and analysis of the activatio= n barriers for isomerization into more stable isomers.
John Keller


=A0
On W= ed, Jul 18, 2012 at 9:42 AM, may abdelghani may01dz[*]yahoo.fr <owner-chemistry\a/ccl.net> wrote:

= Dear CCL'ers

If=A0 the fro= ntier orbital (HOMO's) energy of a compound have a positive= value, is this a conclusive evidence that this compound is a unstable one.


A.May


--20cf307c9fbc3a80fd04c51f3d82-- From owner-chemistry@ccl.net Wed Jul 18 16:02:00 2012 From: "James Stewart mrmopac _ att.net" To: CCL Subject: CCL: positive energy of the frontier orbital Message-Id: <-47229-120718160059-10755-943p0lG8lT2Wmd2K5i+QEA!=!server.ccl.net> X-Original-From: James Stewart Content-Type: multipart/alternative; boundary="2086511853-189085708-1342641651=:49776" Date: Wed, 18 Jul 2012 13:00:51 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: James Stewart [mrmopac(0)att.net] --2086511853-189085708-1342641651=:49776 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable The question was put:"If=A0 thefrontier orbital=0A(HOMO's) energy of a comp= ound have a positive value, is this a conclusive evidence=0Athat this compo= und is a unstable=0Aone."=0A=0AThe answer is, "no!" Compounds with positive= HOMO energies have a tendency to lose electrons, but if a molecule did los= e an electron the resulting cation would likely have a LUMO that was negati= ve, therefore it would be stabilized if it gained an =0Aelectron. So it alw= ays appears that whatever state of ionization it's in, some other state wou= ld be preferable. But whether it did nothing, gained, or lost an electron, = it would still have the same formula, unless there was an additional reacti= on. =0A=0AThe HOMO should not be regarded as a guide to stability, rather s= tability should be regarded as a thermodynamic - kinetic property.=0A=0AMos= t compounds have heats of formation that are negative, some like benzene ha= ve a positive heat of formation.=A0 Benzene's heat of formation is ~+19.8 k= cal/mol (gas phase) or +15.2 kcal/mol (solid), so if it decomposed to graph= ite and hydrogen it would release a lot of energy.=A0 In the lab, benzene i= s nice and stable - the barriers to reaction are so high that the decomposi= tion is kinetically prohibited.=0A=0AJimmy Stewart --2086511853-189085708-1342641651=:49776 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
The quest= ion was put: "= If  the frontier orbital=0A(HOMO's) energy of a compound have a positive value<= /span>, is this a conclusive evidence=0Atha= t this compound is a unstable=0Aone."

The answer is, "no!" Comp= ounds with positive HOMO energies have a tendency to lose electrons,=0A but= if a molecule did lose an electron the resulting cation would likely have= =0A a LUMO that was negative, therefore it would be stabilized if it gained= an =0Aelectron. So it always appears that whatever state of ionization it'= s in, some other state would be preferable. But whether it did nothing, gai= ned, or lost an electron, it would still have the same formula, unless ther= e was an additional reaction.

The HOMO should not be regarded as a = guide to stability, rather stability should be regarded as a thermodynamic = - kinetic property.

Most compounds have heats of formation that are = negative, some like benzene have a positive heat of formation.  Benzen= e's heat of formation is ~+19.8 kcal/mol (gas phase) or +15.2 kcal/mol (sol= id), so if it decomposed to graphite and hydrogen it would release a lot of= energy.  In the lab, benzene is nice and stable - the barriers to rea= ction are so high that the decomposition is kinetically prohibited.

= Jimmy Stewart
--2086511853-189085708-1342641651=:49776-- From owner-chemistry@ccl.net Wed Jul 18 17:02:01 2012 From: "Gustavo L.C. Moura gustavo.moura]*[ufpe.br" To: CCL Subject: CCL: 3D molecular modelling software Message-Id: <-47230-120718170121-9199-nsoB1ZKJYpcdSYSVns4vlQ _ server.ccl.net> X-Original-From: "Gustavo L.C. Moura" Date: Wed, 18 Jul 2012 17:01:18 -0400 Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura.:.ufpe.br] Dear CCL Readers, Would any of you know a molecular modelling software in 3D which can be used to visualize molecules, conformational analysis, molecular dynamics trajectories, docking, etc, using stereo glasses compatible with either NVIDIA 3D Vision or Blu-Ray? Thank you very much in advance. Sincerely yours, Gustavo L.C. Moura From owner-chemistry@ccl.net Wed Jul 18 19:34:00 2012 From: "Andrew Orry andy^_^molsoft.com" To: CCL Subject: CCL: 3D molecular modelling software Message-Id: <-47231-120718193133-17811-2BZu1+asIyv/G9iU9IfMUQ(_)server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 18 Jul 2012 16:36:12 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy..molsoft.com] Gustavo If you have the combination of Nvidia 3D glasses + card + monitor http://www.nvidia.com/object/3d-vision-professional-users.html then MolSoft's ICM-Chemist http://www.molsoft.com/icm-chemist.html , ICM-Chemist-Pro http://www.molsoft.com/icm-chemist-pro.html and other ICM products http://www.molsoft.com/products.html will be able to display 3D . We can send you a license key if you would like to try it. Thanks, Andy -- Andrew Orry Ph.D. MolSoft LLC Senior Research Scientist 11199 Sorrento Valley Road, S209 San Diego CA 92121 USA Tel: 858-625-2000 x108 Fax: 828-625-2888 -- www.molsoft.com www.twitter.com/molsoft On 7/18/2012 2:01 PM, Gustavo L.C. Moura gustavo.moura]*[ufpe.br wrote: > Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura.:.ufpe.br] > Dear CCL Readers, > Would any of you know a molecular modelling software in 3D which can be used to visualize molecules, conformational analysis, molecular dynamics trajectories, docking, etc, using stereo glasses compatible with either NVIDIA 3D Vision or Blu-Ray? > Thank you very much in advance. > Sincerely yours, > Gustavo L.C. Moura> -- Andrew Orry Ph.D. MolSoft LLC Senior Research Scientist 11199 Sorrento Valley Road, S209 San Diego CA 92121 USA Tel: 858-625-2000 x108 Fax: 828-625-2888 -- www.molsoft.com www.twitter.com/molsoft From owner-chemistry@ccl.net Wed Jul 18 20:55:00 2012 From: "Venable, Richard (NIH/NHLBI) E venabler*nhlbi.nih.gov" To: CCL Subject: CCL: 3D molecular modelling software Message-Id: <-47232-120718205357-16019-MTxAZt+X4LwM6c4pQFPJpA-*-server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 18 Jul 2012 20:53:45 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler!A!nhlbi.nih.gov] The PyMol package has some 3D stereo options; see pymol.org -- 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 7/18/12 7:36 PM, "Andrew Orry andy^_^molsoft.com" wrote: > >Sent to CCL by: Andrew Orry [andy..molsoft.com] >Gustavo > >If you have the combination of Nvidia 3D glasses + card + monitor >http://www.nvidia.com/object/3d-vision-professional-users.html >then MolSoft's ICM-Chemist http://www.molsoft.com/icm-chemist.html , >ICM-Chemist-Pro http://www.molsoft.com/icm-chemist-pro.html and other >ICM products http://www.molsoft.com/products.html will be able to >display 3D . > >We can send you a license key if you would like to try it. > >Thanks, >Andy > >-- >Andrew Orry Ph.D. >MolSoft LLC >Senior Research Scientist >11199 Sorrento Valley Road, S209 >San Diego >CA 92121 >USA >Tel: 858-625-2000 x108 >Fax: 828-625-2888 >-- >www.molsoft.com >www.twitter.com/molsoft > > > >On 7/18/2012 2:01 PM, Gustavo L.C. Moura gustavo.moura]*[ufpe.br wrote: >> Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura.:.ufpe.br] >> Dear CCL Readers, >> Would any of you know a molecular modelling software in 3D which >>can be used to visualize molecules, conformational analysis, molecular >>dynamics trajectories, docking, etc, using stereo glasses compatible >>with either NVIDIA 3D Vision or Blu-Ray? >> Thank you very much in advance. >> Sincerely yours, >> Gustavo L.C. Moura> From owner-chemistry@ccl.net Wed Jul 18 21:36:01 2012 From: "Jussi Lehtola jussi.lehtola..helsinki.fi" To: CCL Subject: CCL:G: GaussView Error : CConnectionGFCHK::ParseGFCHK() Message-Id: <-47233-120718195059-24648-wb/Y+s1xcjuSendBtrluLg|a|server.ccl.net> X-Original-From: Jussi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Thu, 19 Jul 2012 02:50:50 +0300 Mime-Version: 1.0 Sent to CCL by: Jussi Lehtola [jussi.lehtola(0)helsinki.fi] On Wed, 18 Jul 2012 10:32:53 +0200 "Javier Cerezo jcb1]=[um.es" wrote: > The problem seem to strive in how gaussview gets the number of > functions to be read, as it apparently get it from "Number of basis > functions" while in the chk file the information refers to the > independent set. Sounds like Gaussian Inc. should really work on their software. This is a rather trivial problem, which can arise already in small molecules with standard basis sets. (clip) > Well, this is just my appreciation (so error-prone) and still did not > answer why one can get such linear dependencies in the basis set. But > hope it gives you an idea to start with. IIRC Szabo & Ostlund has some explanations on this. A most trivial example is a dimer, and very diffuse functions on each atom, say phi_1(r) = exp(-zeta |r-r1|^2) phi_2(r) = exp(-zeta |r-r2|^2) The gaussian exponent zeta establishes a length scale given by L=1/sqrt(zeta). Now, if the internuclear separation |r1-r2| is of the same order of magnitude -- or smaller -- than L, the basis functions will have almost unit overlap. And this gives a linear dependency issue. More generally, one goes into an orthonormal basis given by Cholesky or Löwdin orthogonalization of the overlap matrix. If linear dependencies are an issue, you can use canonical orthogonalization: find out the eigenvectors and eigenvalues of the overlap matrix and throw away the eigenvectors with eigenvalues smaller than 10^-5. -- -------------------------------------------------------- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.lehtola * helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol University of Helsinki Office phone: +358 9 191 50 632 Finland -------------------------------------------------------- Jussi Lehtola, FM Tohtorikoulutettava jussi.lehtola * helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto Työpuhelin: (0)9 191 50 632 -------------------------------------------------------- From owner-chemistry@ccl.net Wed Jul 18 22:11:00 2012 From: "mark94025*comcast.net" To: CCL Subject: CCL: 3D molecular modelling software Message-Id: <-47234-120718201852-4362-I7FamLqNVrMKDXxvZSjveg+*+server.ccl.net> X-Original-From: mark94025:comcast.net Content-Type: multipart/alternative; boundary="----=_Part_84023_37186311.1342657125088" Date: Thu, 19 Jul 2012 00:18:45 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: mark94025+/-comcast.net ------=_Part_84023_37186311.1342657125088 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit VMD ----- Original Message ----- > From: Gustavo L.C. Moura gustavo.moura]*[ufpe.br To: Mark Berger Sent: Wed, 18 Jul 2012 21:01:18 -0000 (UTC) Subject: CCL: 3D molecular modelling software Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura.:.ufpe.br] Dear CCL Readers, Would any of you know a molecular modelling software in 3D which can be used to visualize molecules, conformational analysis, molecular dynamics trajectories, docking, etc, using stereo glasses compatible with either NVIDIA 3D Vision or Blu-Ray? Thank you very much in advance. Sincerely yours, Gustavo L.C. Mourahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------=_Part_84023_37186311.1342657125088 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable VMD

----- Original Message -----=
From: Gustavo L.C. Moura gustavo.moura]*[ufpe.br <owner-chemistry_._cc= l.net>
To: Mark Berger <mark94025_._comcast.net>
Sent= : Wed, 18 Jul 2012 21:01:18 -0000 (UTC)
Subject: CCL: 3D molecular model= ling software


Sent to CCL by: "Gustavo L.C. Moura" [gustavo.mour= a.:.ufpe.br]
Dear CCL Readers,
     Would any of = you know a molecular modelling software in 3D which can be used to visualiz= e molecules, conformational analysis, molecular dynamics trajectories, dock= ing, etc, using stereo glasses compatible with either NVIDIA 3D Vision or B= lu-Ray?
Thank you very much in advance.
Sincerely yours,
 &nb= sp;           Gustavo L.C= . Moura



-=3D This is automatically added to each message by = the mailing script =3D-
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------=_Part_84023_37186311.1342657125088-- From owner-chemistry@ccl.net Wed Jul 18 22:46:00 2012 From: "Marc-Andr B langer marc-andre.belanger- -umontreal.ca" To: CCL Subject: CCL: Haskell in Computational Chemistry Message-Id: <-47235-120718202906-8973-Rvzsb2Isti43yk1KUovmsA**server.ccl.net> X-Original-From: "Marc-Andr B langer" Date: Wed, 18 Jul 2012 20:29:04 -0400 Sent to CCL by: "Marc-Andr B langer" [marc-andre.belanger(-)umontreal.ca] Hi CCL, I am currently learning Haskell. It is a very interesting language, and I feel there is potential to do good work with it. I am wondering if any of you already use Haskell for work, or know of any projects using it? I know there's a QM package available in the Hackage repository, but I haven't tried it yet - I'm still fighting through the tutorials. Comments and opinions are appreciated. Marc-Andr Blanger marc-andre.belanger(!)umontreal.ca From owner-chemistry@ccl.net Wed Jul 18 23:20:00 2012 From: "Frank Jensen frj[]chem.au.dk" To: CCL Subject: CCL: positive energy of the frontier orbital Message-Id: <-47236-120718195701-26904-JgQ3z0Koi+41aPndmjrwpw[A]server.ccl.net> X-Original-From: Frank Jensen Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 19 Jul 2012 01:56:51 +0200 MIME-Version: 1.0 Sent to CCL by: Frank Jensen [frj#,#chem.au.dk] A positiv HOMO energy means that the total energy can be lowered by removing some of the electron density. A free electron has an 'orbital' energy of zero, thus in a sufficiently flexible basis set, the electron density in the HOMO can be transfered to a free electron state, and give a lower energy state. This is common when using DFT for anions, where transfer of a fraction of the HOMO density to an unbound electron 'orbital' gives a lower energy state. Note that a 'sufficiently flexible basis set' is not just your favorite basis set augmented with diffuse functions, it must contain diffuse functions with exponents in ~10^-4 or less range. Frank Citat af "may abdelghani may01dz[*]yahoo.fr" : > > > Dear CCL'ers > If  the frontier orbital > (HOMO's) energy of a compound have a positive value, is this a > conclusive evidence > that this compound is a unstable > one. > A.May > > Frank Jensen Assoc. Prof. Dept. of Chemistry Aarhus University http://old.chem.au.dk/~frj