From owner-chemistry@ccl.net Mon Apr 13 01:03:01 2009 From: "Sharan sara180681[]gmail.com" To: CCL Subject: CCL:G: Please Help me NMR INPUT FILE FOR GAUSSAIN 03 Message-Id: <-39069-090413010122-16083-TnZ4JD7oCCQaichyG6JrOA(a)server.ccl.net> X-Original-From: Sharan Content-Type: multipart/alternative; boundary=000e0cd147103df87d0467689a87 Date: Mon, 13 Apr 2009 10:31:08 +0530 MIME-Version: 1.0 Sent to CCL by: Sharan [sara180681__gmail.com] --000e0cd147103df87d0467689a87 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear luisfer First i would like to thank you for your interest in replying for my mail. 1) Please correct me if i am wrong, in the below mention input file, if i want to specify C13 how can i do that. 2) How to specify the solvent in which i would like to take the NMR where i= s the options to do this...... --=20 SARAVANAN.I Jr. Scientist Chemoinformatics On Sat, Apr 11, 2009 at 3:34 AM, luisfer**edu.xunta.es < owner-chemistry*o*ccl.net> wrote: > > Sent to CCL by: [luisfer|,|edu.xunta.es] > Dear Sarah. > An example of input file for NMR calculatios can be as: > > %chk=3D ... > %mem=3D ... mb > %nproc=3D ... > # nmr=3D( {nmr-method},spinspin,mixed) rb3lyp/6311++G(3df,3pd) > > charge multiplicity > atom 1 x1 y1 z1 > atom 2 x2 y2 z2 > . > . > . > atom n xn yn zn > > atom 1 atomic mass of 1 > atom 2 atomic mass of 2 > . . . > . . . > . . . > atom n atomic mass of n > > I hope it can help you. > Best regards. > > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D > Luis F. R. V=E1zquez > Real Sociedad Espa=F1ola de Qu=EDmica > Grupo de F=EDsica At=F3mica y Molecular > R=FAa Tornos, 21, piso 3 > 15007 A Coru=F1a-GALICIA-SPAIN > Tel. +34676300472 > Correo-e luisfer*o*edu.xunta.es > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D > > ----- Mensaxe orixinal ----- > De: "Sharan sara180681^gmail.com" > Data: Venres, Abril 10, 2009 6:51 am > Asunto: CCL:G: Please Help me NMR INPUT FILE FOR GAUSSAIN 03 > > > Dear Friends > > > > I am new to Gaussian i am doing my research > > in spectroscopy investigation using Gaussian. I am struck in giving > > NMRinput file for Gaussian. > > > > 1) How to specify the isotopes > > 2) How to change the solvents for NMR > > > > I don't know how to specify these requirements while giving NMR > > Input. Is > > there somebody to give hand to my problem , it will helpful for me... > > > > Advance thanks > > -- > > SARAVANAN.I > > Jr. Scientist Chemoinformatics > > > > > > - This is automatically added to each message by the mailing script -> > > --000e0cd147103df87d0467689a87 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear=A0luisfer

First i would like to thank you for your = interest in replying for my mail.

1) Please correc= t me if i am wrong, =A0in the below mention input file, if i want to specif= y C13 how can i do that.

2) How to=A0specify=A0the solvent in which i would like= to take the NMR where is the options to do this......

--=A0
SARAVANAN= .I=A0
Jr. Scientist Chemoinformatics

On Sat, Apr 11, 2009 at 3:34 AM, luisfer**edu.xunta.es <owne= r-chemistry*o*ccl.net> wrote:

Sent to CCL by: [luisfer|,|edu.xunta.es]
Dear Sarah.
An example of input file for NMR calculatios can be as:

%chk=3D ...
%mem=3D ... mb
%nproc=3D ...
# nmr=3D( {nmr-method},spinspin,mixed) rb3lyp/6311++G(3df,3pd)

charge multiplicity
atom 1 =A0x1 =A0 y1 =A0 z1
atom 2 =A0x2 =A0 y2 =A0 z2
.
.
.
atom n xn =A0yn =A0zn

atom 1 atomic mass of 1
atom 2 atomic mass of 2
=A0 =A0. =A0 =A0 =A0 =A0 =A0. =A0 =A0 =A0 =A0 =A0.
=A0 =A0. =A0 =A0 =A0 =A0 =A0. =A0 =A0 =A0 =A0 =A0.
=A0 =A0. =A0 =A0 =A0 =A0 =A0. =A0 =A0 =A0 =A0 =A0.
atom n atomic mass of n

I hope it can help you.
Best regards.

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D
Luis F. R. V=E1zquez
Real Sociedad Espa=F1ola de Qu=EDmica
Grupo de F=EDsica At=F3mica y Molecular
R=FAa Tornos, 21, piso 3
15007 A Coru=F1a-GALICIA-SPAIN
Tel. +34676300472
Correo-e luisfer*o*= edu.xunta.es
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D

----- Mensaxe orixinal -----
De: "Sharan sara180681^= gmail.com" <owner-chemistry*o*ccl.net>
Data: Venres, Abril 10, 2009 6:51 am
Asunto: CCL:G: Please Help me NMR INPUT FILE FOR GAUSSAIN 03

> Dear Friends
>
> I am new to Gaussian i am doing my research
> in spectroscopy investigation using Gaussian. I am struck in giving > NMRinput file for Gaussian.
>
> 1) =A0How to specify the isotopes
> 2) How to change the solvents for NMR
>
> I don't know how to specify these requirements while giving NMR > Input. Is
> there somebody to give hand to my problem , it will helpful for me...<= br> >
> Advance thanks
> --
> SARAVANAN.I
> Jr. Scientist Chemoinformatics
>



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--000e0cd147103df87d0467689a87-- From owner-chemistry@ccl.net Mon Apr 13 07:51:01 2009 From: "mi yang agri_chemist#yahoo.com" To: CCL Subject: CCL: NLO calculation with solvent effects Message-Id: <-39070-090413074814-18570-gHGqa4PijV0577EZP92P/A(a)server.ccl.net> X-Original-From: "mi yang" Date: Mon, 13 Apr 2009 07:48:10 -0400 Sent to CCL by: "mi yang" [agri_chemist]=[yahoo.com] Hello CCL user, I would like to ask sth about NLO property in soln. I want to calculate First hyperpolarizability (Beta) with solvent effects. There are two possible ways: 1- To put the polar key word in the same input section as for Solvent effect but this gives me very large value 2- To re-optimized the geometry of the molecule with solvent effect and then re-calculate the NLO value on this relaxed geomtry. Now, I am wondering, which method is right for taking the solvent effect in calculation of beta value... thanx for any comment Miyang From owner-chemistry@ccl.net Mon Apr 13 09:16:00 2009 From: "=?utf-8?B?cGlhb3hx?= piaoxq[A]cm.kyushu-u.ac.jp" To: CCL Subject: CCL: =?utf-8?B?Y2FsY3VsYXRpb24gb2YgdGhlIGZpcnN0IGh5cGVycG9sYXJpemFiaWxpdHksICAgYXNrIGZvciBoZWxwLS0tLS0tLS0tdGhhbmsgeW91IHNvIG11Y2guIA==?= Message-Id: <-39071-090413072045-187041-3hQ1sqbLGWEkS64JajNzDQ*|*server.ccl.net> X-Original-From: "=?utf-8?B?cGlhb3hx?=" Content-Type: multipart/alternative; boundary="=====003_Dragon226144255548_=====" Date: Mon, 13 Apr 2009 19:04:36 +0900 Mime-Version: 1.0 Sent to CCL by: "=?utf-8?B?cGlhb3hx?=" [piaoxq|*|cm.kyushu-u.ac.jp] This is a multi-part message in MIME format. --=====003_Dragon226144255548_===== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 IERlYXIgY2NsJ2Vycw0KDQoNCiAgICAgICAgSSB3YW50IHRvIGtub3cgaG93IHRvIHRyYW5zbGF0 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QGdtYWlsLmNvbTwvQT48L0RJVj4NCjxESVY+PEZPTlQgDQpjb2xvcj0jODA4MDgwPioqKioqKioq KioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKio8L0ZP TlQ+PC9ESVY+PC9GT05UPjwvRElWPjwvRk9OVD48L0RJVj48L0ZPTlQ+PC9CT0RZPjwvSFRNTD4N Cg== --=====003_Dragon226144255548_=====-- From owner-chemistry@ccl.net Mon Apr 13 14:30:01 2009 From: "Rudolph J. Magyar rjmagya++sandia.gov" To: CCL Subject: CCL: VASP LOPTICS = .TRUE. Message-Id: <-39072-090413122451-2395-1dQQruvhX9oH8YpCgNXf7Q]_[server.ccl.net> X-Original-From: "Rudolph J. Magyar" Date: Mon, 13 Apr 2009 12:24:47 -0400 Sent to CCL by: "Rudolph J. Magyar" [rjmagya---sandia.gov] Hi, Does any one know how to get vasp to output the imaginary part of epsilon within TDDFT? I've tried fiddling with LRPA but this doesn't seen to have much of an effect. Thanks, Rudy From owner-chemistry@ccl.net Mon Apr 13 15:06:01 2009 From: "Rudolph J. Magyar rjmagya-#-sandia.gov" To: CCL Subject: CCL: VASP GW Message-Id: <-39073-090413122727-2683-bk7T2P5lNnGLZAVMMHZmIg###server.ccl.net> X-Original-From: "Rudolph J. Magyar" Date: Mon, 13 Apr 2009 12:27:23 -0400 Sent to CCL by: "Rudolph J. Magyar" [rjmagya(0)sandia.gov] Hi, Does any one know how to run GW calculations on VASP? Do you have a sample input file? Thanks, Rudy From owner-chemistry@ccl.net Mon Apr 13 15:56:01 2009 From: "veronica ferraresi veroferraresi-x-gmail.com" To: CCL Subject: CCL:G: chemcraft, cubegen and density Message-Id: <-39074-090413154019-28792-XFmqvb1kHyxRkJjJwGaucQ=server.ccl.net> X-Original-From: veronica ferraresi Content-Type: multipart/alternative; boundary=0016e644cf5c17cc6b046774e167 Date: Mon, 13 Apr 2009 16:39:57 -0300 MIME-Version: 1.0 Sent to CCL by: veronica ferraresi [veroferraresi+/-gmail.com] --0016e644cf5c17cc6b046774e167 Content-Type: text/plain; charset=GB2312 Content-Transfer-Encoding: quoted-printable Hello, It is not clear from your email if you need spin density or total density. To generate the cubefile: *cubegen** memory kind fchkfile cubefile npts format* The parameters, which are not case-sensitive, have the following meanings: *memory* Amount of dynamic memory to allocate in words. A value of *0* implies a machine-specific default value. *kind* A keyword specifying the type of cube to generate *MO=3D**n*: Molecular orbital *n*. The keywords *Homo*, *Lumo*, *All*, *OccA*(all alpha occupied), *OccB *(all beta occupied), *Valence* (all valence orbitals) and *Virtuals*(all virtual orbitals) may also be used in place of a specific orbital number. There is no default for *n*, and an error will occur if it is omitted. * Density=3D**type*: Total density of the specified type. *Spin=3D**type*: Spin density (difference between =A6=C1 and =A6=C2 densiti= es) of the specified type. *Alpha=3D**type: *Alpha spin density of the specified type. *Beta=3D**type: *Beta spin density of the specified type.* * *Potential=3D**type: *Electrostatic potential using the density of the specified type. The *type* keyword is one of the single density selection options that are valid with the *Density *keywor= d: *SCF*, *MP2*, *CI*, *QCI*, and so on (note that *Current* is not supported)= . The *fdensity*, *falpha* and *fbeta* forms request the use of full instead of frozen-core densities. The default is *SCF*. I copied all that from Gaussian help. Ver=A8=AEnica. 2009/4/12 Madi madi7sk]^[gmail.com > > Sent to CCL by: Madi [madi7sk]*[gmail.com] > Hi David, > > It says "Electron density from Total SCF Density" on the left work area. > Is there a command line that i need to use during the making of cube file > to get "electron density from spin"?. I tried changing the contour value = to > 0.0008. the blob gets much bigger. when I go to higher contour values, > size of the blobs become smaller. The blob stays in single colour though. > There are other parameters such as values range and scale. Are there > appropriate > settings for those that i need to use? > > Thank you for your help > Madi > > On Sun, Apr 12, 2009 at 2:22 PM, Close, David M. CLOSED##mail.etsu.edu > wrote: > > > > Sent to CCL by: "Close, David M." [CLOSED(0)mail.etsu.edu] > > Madi: > > When you open the .cube file, does a work area appear on the left that > says "Electron Density from Spin" ? If so, move down to the choice "Show > Isosurface, and then click on the "Both Signed" option to the right. You > still may not see what you want because the Contour Value is too big. Cl= ick > on the Contour Value to make it below say 0.0008, and you should see > positive and negative spin densities. > > Regards, Dave Close. > > > > -----Original Message----- > >> From: owner-chemistry+closed=3D=3Detsu.edu**ccl.net [mailto: > owner-chemistry+closed =3D=3Detsu.edu**ccl.net]= On > Behalf Of Madi madi7sk _ gmail.com > > Sent: Saturday, April 11, 2009 11:38 AM > > To: Close, David M. > > Subject: CCL: chemcraft, cubegen and density > > > > > > Sent to CCL by: Madi [madi7sk-.-gmail.com] > > Hi All > > I am sorry about not wording the question properly. > > I meant to ask how to see regions of high and low electron densities. > > Right now i am able to see only one colored blob on the molecule. > > > > Thanks > > madi > > On Sat, Apr 11, 2009 at 9:53 AM, Madhavan Narayanan > > madi7sk_._gmail.com wrote: > >> > >> Sent to CCL by: "Madhavan Narayanan" [madi7sk * gmail.com] > >> Hi, > >> > >> I converted my check point file to .fchk and then to .cube. > >> Then I tried opening it in chemcraft. When I opened it to view the > electron density, I see only atoms with positive density. How do I get it= to > show me both positive and negative regions? I am very new to this and wou= ld > appreciate any help. > >> > >> Thank you > >> Madi > >> > >> > >> > >> -=3D This is automatically added to each message by the mailing script= =3D-> > >> > >> > > > > > > > > -- > > > > > > > > -=3Dhis is automatically added to each message by the mailing script = =3DJob: > http://www.ccl.net/jobs> > > > > - This is automatically added to each message by the mailing script -> > > > > > > > > - This is automatically added to each message by the mailing script -> > > --0016e644cf5c17cc6b046774e167 Content-Type: text/html; charset=GB2312 Content-Transfer-Encoding: quoted-printable Hello,
It is= not clear from your email if you need spin density or total density.
To generate the cubefile:
cubegen  memory kind fchkfile cubefile npts format
<=
/span>

The parameters, which are not case-sensitive, have the following meanings:<=
/span>

memory Amount of dynamic memory to allocate in words. A value of 0 implies = a machine-specific default value.

kind
A keyword specifying the type of cube to generate

MO=3Dn<= span style=3D"" lang=3D"EN-US">: Molecular orbital n. The keywords <= b>Homo, Lumo, All, OccA (all alpha occupied), OccB (all beta occupied), Valence (all valence orbitals) and Virtuals (all virtual orbitals) may also = be used in place of a specific orbital number. There is no default for n, and an error will occur if it is omitted.

Density=3Dtype: Total density of the specified type.

Spin=3Dtype: Spin density (difference = between =A6=C1 and =A6=C2 densities) of the specified type.

Alpha=3Dtype: Alpha spin density of th= e specified type.

Beta=3Dtype: Beta spin density of the = specified type.=

Potential=3D<= span style=3D"font-size: 12pt;" lang=3D"EN-US">type: Electrostat= ic potential using the density of the specified type.

The type keyword is one of the single density selection options that are valid with the Density keyword: = SCF, MP2, CI, QCI, and so on (note that Current is not supported). The fdensity, falpha a= nd fbeta forms request the use of full instead of frozen-core densities. The default= is SCF.

I copied all that from Gaussian help.

Ver=A8=AEnica.


2009/4/12 Madi ma= di7sk]^[gmail.com <owner-chemistry*|*ccl.net>

Sent to CCL by: Madi [madi7sk]*[gmail.com]
Hi David,

It says "Electron density from Total SCF Density" on the left wor= k area.
Is there a command line that i need to use during the making of cube file to get "electron density from spin"?. I tried changing the contou= r value to
0.0008. the blob gets much bigger. when I go to higher contour values,
size of the blobs become smaller. The blob stays in single colour though. There are other parameters such as values range and scale.  Are there<= br> appropriate
settings for those that i need to use?

Thank you for your help
Madi

On Sun, Apr 12, 2009 at 2:22 PM, Close, David M. CLOSED##mail.etsu.edu
<owner-chemistry+/-ccl.net> wrote:
>
> Sent to CCL by: "Close, David M." [CLOSED(0)mail.etsu.edu]
> Madi:
>  When you open the .cube file, does a work area appear on the lef= t that says "Electron Density from Spin" ?  If so, move down= to the choice "Show Isosurface, and then click on the "Both Sign= ed" option to the right.  You still may not see what you want bec= ause the Contour Value is too big.  Click on the Contour Value to make= it below say 0.0008, and you should see positive and negative spin densiti= es.
>  Regards, Dave Close.
>
> -----Original Message-----
>> From: owner-chemistry+closed=3D=3Detsu.edu**cc= l.net [mailto:owner-chemist= ry+closed=3D=3Detsu.edu**ccl.net] On Behalf Of = Madi madi7sk _ gmail.com=
> Sent: Saturday, April 11, 2009 11:38 AM
> To: Close, David M.
> Subject: CCL: chemcraft, cubegen and density
>
>
> Sent to CCL by: Madi [madi7sk-.-gmail.com]
> Hi All
> I am sorry about not wording the question properly.
> I meant to ask how to see regions of high and low electron densities.<= br> > Right now i am able to see only one colored blob on the molecule.
>
> Thanks
> madi
> On Sat, Apr 11, 2009 at 9:53 AM, Madhavan Narayanan
> madi7sk_._gmail.com= <owner-chemistry[#]ccl.net= > wrote:
>>
>> Sent to CCL by: "Madhavan  Narayanan" [madi7sk * gmail.com]
>> Hi,
>>
>> I converted my check point file to .fchk and then to .cube.
>> Then I tried opening it in chemcraft. When I opened it to view the= electron density, I see only atoms with positive density. How do I get it = to show me both positive and negative regions? I am very new to this and wo= uld appreciate any help.
>>
>> Thank you
>> Madi
>>
>>
>>
>> -=3D This is automatically added to each message by the mailing sc= ript =3D->      http://www.ccl.net/cgi-bin/ccl/send_cc= l_message>      http://www.ccl.net/cgi-bin/ccl/sen= d_ccl_message>      http://www.ccl.net/chemistry/sub_= unsub.shtml>      http://www.ccl.net/spammers.txt>
>>
>>
>
>
>
> --
>
>
>
> -=3Dhis is automatically added to each message by the mail= ing script =3Dhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messageJob:= http://www.ccl.net/j= obs>
>
> - This is automatically added to each message by the mailing script -&= gt;      http://www.ccl.net/cgi-bin/ccl/send_ccl_message<= /a>>      http://www.ccl.net/cgi-bin/ccl/send_ccl_mess= age>      http://www.ccl.net/chemistry/sub_unsub.shtm= l>      http://www.ccl.net/spammers.txt>
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>




--0016e644cf5c17cc6b046774e167-- From owner-chemistry@ccl.net Mon Apr 13 23:29:01 2009 From: "Duy Le ttduyle*_*gmail.com" To: CCL Subject: CCL: Opendx binary for windows Message-Id: <-39075-090413232753-8281-5yEiJFSpWRD6xA5X8eka8w::server.ccl.net> X-Original-From: "Duy Le" Date: Mon, 13 Apr 2009 23:27:50 -0400 Sent to CCL by: "Duy Le" [ttduyle-.-gmail.com] Dear CCLers, Opendx's host (at sdsc.edu) is stop working for awhile. I am in need of redownloading again Opendx binary for windows. I truly appreciate If anyone can help me to put it in your host with downloadable link, for example http://www.yousendit.com/ or tell me how to get one. Thanks Duy.