From owner-chemistry@ccl.net Thu Feb 3 01:45:01 2011 From: "Krishna Kuben Govender kk.govender^gmail.com" To: CCL Subject: CCL:G: UV/VIS Gaussian09 Message-Id: <-43840-110203013835-15943-RXINqWe0yeRuXOngZuUwVw : server.ccl.net> X-Original-From: "Krishna Kuben Govender" Date: Thu, 3 Feb 2011 01:38:34 -0500 Sent to CCL by: "Krishna Kuben Govender" [kk.govender^_^gmail.com] Good day everyone, I trust that there is someone who maybe able to aid me with a problem I am having regarding the generation of UV/Vis spectra using Gaussian 09. I have fairly large Iron (Fe) system which I have successfully optimized and confirmed that it lies at a minima on the potential energy surface by generating the Frequencies for this optimized molecule. I then took the above mentioned system and submitted it for a single point time dependent simulation using the following input: # OPBE/ChkBasis NoSymm Guess=Read Geom=allcheck TD(NState=5) The simulation runs for a short while, but then crashes out with the following warning and error, respectively: Warning: The smallest alpha delta epsilon is .... Fatal Problem: The smallest beta delta epsilon is .... Can anyone provide me with some solutions to my problem. I would really appreciate any help with the matter, especially since this is the first time that I am trying to carry out simulations of this nature. Thanks in advance for your help. Regards, Krishna Kuben Govender PhD Graduate Student University of Cape Town Scientific Computing Research Unit From owner-chemistry@ccl.net Thu Feb 3 02:20:01 2011 From: "osama T Akoubeh dolkeen_+_hotmail.com" To: CCL Subject: CCL:G: Aplying basis set in gaussian Message-Id: <-43841-110203015518-20426-K0tjHtO96vva6ELg95eDbw,+,server.ccl.net> X-Original-From: "osama T Akoubeh" Date: Thu, 3 Feb 2011 01:55:17 -0500 Sent to CCL by: "osama T Akoubeh" [dolkeen=hotmail.com] Hi How to put following basis set in calculation using Gaussian using DFT B3LYP-6-31G++ and B3LYP-6-31+G++ Thanks O.Akoubeh From owner-chemistry@ccl.net Thu Feb 3 02:55:01 2011 From: "bonoit bonoit bonoit_10(!)yahoo.fr" To: CCL Subject: CCL: Geometrical parameters Message-Id: <-43842-110203022311-26428-biu6mXxyruqyiyLnuwqQDw:_:server.ccl.net> X-Original-From: "bonoit bonoit" Date: Thu, 3 Feb 2011 02:23:10 -0500 Sent to CCL by: "bonoit bonoit" [bonoit_10[-]yahoo.fr] Dear CCLers, I need a software which is used to set geometrical parameters on a structure to get an image on which we can see the structure (ball and stick) and its geometrical parameters. I try chemoffice but it doesn't work. Your help will be the most appreciated Sincerely bonoit From owner-chemistry@ccl.net Thu Feb 3 05:32:00 2011 From: "Alex Naden anaden===fsmail.net" To: CCL Subject: CCL: Large .XYZ file visualization Message-Id: <-43843-110203052955-8126-AE8wisDk/WWA1+psRDEaTA(!)server.ccl.net> X-Original-From: "Alex Naden" Date: Thu, 3 Feb 2011 05:29:53 -0500 Sent to CCL by: "Alex Naden" [anaden*fsmail.net] Hello All, Thank you for your replies and suggestions. Just to expand on my original question: I am trying to look at the .xyz files containing 25000 of atoms and more. I have tried opening them in several freeware Lunux based programs before posting the question on the forum but without much success, as the structures were loaded for an indefinite length of time (well in excess of two hours). I am not sure whether it is partially to do with my machine spec (Intel Pentium 4, 1 Gb memory) or the inability of the programs that I have picked to handle this amount of atoms. Hence, was my question on the forum. I am going to try the suggested programs. Thank you all for your help. Alex From owner-chemistry@ccl.net Thu Feb 3 07:26:00 2011 From: "Marcel Swart marcel.swart###icrea.cat" To: CCL Subject: CCL: Large .XYZ file visualization Message-Id: <-43844-110203072211-15869-8BGWz6bLCrYazSdRpU+21A^^server.ccl.net> X-Original-From: Marcel Swart Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 3 Feb 2011 13:21:58 +0100 Mime-Version: 1.0 (Apple Message framework v1082) Sent to CCL by: Marcel Swart [marcel.swart=-=icrea.cat] Hi Alex, I think you should be careful, normally people use PDB files that contain not only the atomic coordinates, but also residue names and numbers; this makes the visualization of e.g. proteins quite easy using e.g. VMD, Rasmol, etc. This is in part also because the connection tables are known for most of the residues; in principle, if you just give the program xyz files with atomic coordinates, it has to find out these connections (which can be done, but may take some time). Marcel On Feb 3, 2011, at 11:29 AM, Alex Naden anaden===fsmail.net wrote: > Hello All, > > Thank you for your replies and suggestions. > > Just to expand on my original question: > > I am trying to look at the .xyz files containing 25000 of atoms and more. I have tried opening them in several freeware Lunux based programs before posting the question on the forum but without much success, as the structures were loaded for an indefinite length of time (well in excess of two hours). I am not sure whether it is partially to do with my machine spec (Intel Pentium 4, 1 Gb memory) or the inability of the programs that I have picked to handle this amount of atoms. Hence, was my question on the forum. > > I am going to try the suggested programs. > > Thank you all for your help. > > Alex =================================== dr. Marcel Swart ICREA Research Professor at Institut de Química Computacional Universitat de Girona Facultat de Cičncies Campus Montilivi 17071 Girona Catalunya (Spain) tel +34-972-418861 fax +34-972-418356 e-mail marcel.swart * icrea.cat marcel.swart * udg.edu web http://www.marcelswart.eu =================================== From owner-chemistry@ccl.net Thu Feb 3 08:01:00 2011 From: "Close, David M. CLOSED[#]mail.etsu.edu" To: CCL Subject: CCL:G: Aplying basis set in gaussian Message-Id: <-43845-110203074348-28790-IzrrMKdTDfXTv5SN35uc8A::server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 3 Feb 2011 12:43:35 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED(a)mail.etsu.edu] Osama: In the Gaussian suite of programs are about 400 test examples. Look at any of these examples. You will see that the first few lines begin with %chk=, or %Mem=, etc. Then you will see a line that begins with #. This line has the basis set on it as in #B3LYP/6-31G**, followed by keywords to denote the type of job you wish to run. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed==etsu.edu^ccl.net [mailto:owner-chemistry+closed==etsu.edu^ccl.net] On Behalf Of osama T Akoubeh dolkeen_+_hotmail.com Sent: Thursday, February 03, 2011 1:55 AM To: Close, David M. Subject: CCL:G: Aplying basis set in gaussian Sent to CCL by: "osama T Akoubeh" [dolkeen=hotmail.com] Hi How to put following basis set in calculation using Gaussian using DFT B3LYP-6-31G++ and B3LYP-6-31+G++ Thanks O.Akoubehhttp://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 Thu Feb 3 08:35:01 2011 From: "Alexander Klenner alexander.klenner++pharma.ethz.ch" To: CCL Subject: CCL: Large .XYZ file visualization Message-Id: <-43846-110203043222-13145-8/D/dF8hDclIKDUE5T3HnA[#]server.ccl.net> X-Original-From: Alexander Klenner Content-Type: multipart/alternative; boundary="Apple-Mail-344-590753501" Date: Thu, 3 Feb 2011 10:32:13 +0100 MIME-Version: 1.0 (Apple Message framework v1082) Sent to CCL by: Alexander Klenner [alexander.klenner|*|pharma.ethz.ch] --Apple-Mail-344-590753501 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Hi Alex, you could try paraview. http://www.paraview.org/ Alex Am 02.02.2011 um 13:59 schrieb Alex Naden anaden],[fsmail.net: >=20 > Sent to CCL by: "Alex Naden" [anaden,+,fsmail.net] > Hello, >=20 > Could anyone recommend a software (Linux/ Windows) or on-line that is = capable of handling very large .xyz files?=20 >=20 > Thank you, >=20 > Alex >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 -- ETH Zurich Dipl.-Bioinf. Alexander G. Klenner Institute of Pharmaceutical Sciences HCI G 496 Wolfgang-Pauli-Str. 10 8093 Z=FCrich SWITZERLAND +41 44 633 74 23 phone _________________________________________________________=20 Confidentiality Note: This message is intended only for the use of the = named recipients and may contain confidential and/or privileged = information. If you are not the intended recipient, please contact the = sender and delete this message. Any unauthorized use of the information = contained in this message is prohibited. --Apple-Mail-344-590753501 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="iso-8859-1" Hi = Alex,

you could try = paraview.

<= br>
Alex

Am 02.02.2011 um 13:59 = schrieb Alex Naden anaden],[fsmail.net:


Sent to CCL by: "Alex  Naden" = [anaden,+,fsmail.net]
Hello,

Could anyone recommend a software = (Linux/ Windows) or on-line that is capable of handling very large .xyz = files?

Thank you,

Alex



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= --Apple-Mail-344-590753501-- From owner-chemistry@ccl.net Thu Feb 3 09:10:01 2011 From: "Ian Grant Ian.Grant(0)ruhr-uni-bochum.de" To: CCL Subject: CCL: Large .XYZ file visualization Message-Id: <-43847-110203065332-30310-qPJQZTh3jhbG9rk2o3T/+w-#-server.ccl.net> X-Original-From: "Ian Grant" Content-Type: multipart/alternative; boundary="------------060900040201010209080406" Date: 3 Feb 2011 12:53:23 +0100 MIME-Version: 1.0 Sent to CCL by: "Ian Grant" [Ian.Grant|ruhr-uni-bochum.de] This is a multi-part message in MIME format. --------------060900040201010209080406 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit How many frames does the trajectory contain? As someone else indicated, the number of atoms per frame and number of frames together determine the size and therefore memory requirements. If you're loading it in VMD, try selecting 'load all at once' rather than 'load in background' (which is the default I think). Alternatively, you could use CatDCD to trim the trajectory down, either by extracting only every nth frame (the 'stride'), or a subset of the atoms (with an 'index'). E.g. if you have water molecules, often you're not bothered about visualizing those. Ian On 03/02/11 11:29, Alex Naden anaden===fsmail.net wrote: > Sent to CCL by: "Alex Naden" [anaden*fsmail.net] > Hello All, > > Thank you for your replies and suggestions. > > Just to expand on my original question: > > I am trying to look at the .xyz files containing 25000 of atoms and more. I have tried opening them in several freeware Lunux based programs before posting the question on the forum but without much success, as the structures were loaded for an indefinite length of time (well in excess of two hours). I am not sure whether it is partially to do with my machine spec (Intel Pentium 4, 1 Gb memory) or the inability of the programs that I have picked to handle this amount of atoms. Hence, was my question on the forum. > > I am going to try the suggested programs. > > Thank you all for your help. > > Alex> > -- ------------------------------------------------------------------------ Dr. Ian M. Grant [ian.grant+*+ruhr-uni-bochum.de] Centre for Theoretical Chemistry Ruhr-Universität Bochum 44780 Bochum, Germany Office: NC 03/51 --- Tel.: +49 234 32 26751 --------------060900040201010209080406 Content-Type: multipart/related; boundary="------------020706060506060209050204" --------------020706060506060209050204 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit How many frames does the trajectory contain? As someone else indicated, the number of atoms per frame and number of frames together determine the size and therefore memory requirements.

If you're loading it in VMD, try selecting 'load all at once' rather than 'load in background' (which is the default I think).

Alternatively, you could use CatDCD to trim the trajectory down, either by extracting only every nth frame (the 'stride'), or a subset of the atoms (with an 'index'). E.g. if you have water molecules, often you're not bothered about visualizing those.

Ian



On 03/02/11 11:29, Alex Naden anaden===fsmail.net wrote: 
Sent to CCL by: "Alex  Naden" [anaden*fsmail.net]
Hello All,

Thank you for your replies and suggestions. 

Just to expand on my original question:

I am trying to look at the .xyz files containing 25000 of atoms and more. I have tried opening them in several freeware Lunux based programs before posting the question on the forum but without much success, as the structures were loaded for an indefinite length of time (well in excess of two hours). I am not sure whether it is partially to do with my machine spec (Intel Pentium 4, 1 Gb memory) or the inability of the programs that I have picked to handle this amount of atoms. Hence, was my question on the forum. 

I am going to try the suggested programs.

Thank you all for your help.

AlexE-mail to subscribers: CHEMISTRY+*+ccl.net or use:
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Dr. Ian M. Grant [ian.grant+*+ruhr-uni-bochum.de]
Centre for Theoretical Chemistry
Ruhr-Universität Bochum
44780 Bochum, Germany
Office: NC 03/51 — Tel.: +49 234 32 26751
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I think this will give 5 instead of the default 2 digits beyond to decimal separator. Steve Williams ----- Original Message ----- > From: "Eduard Matito ematito..gmail.com" Date: Wednesday, February 2, 2011 9:13 am Subject: CCL:G: number of digits in Gaussian output To: "Williams, Steve " > > Sent to CCL by: Eduard Matito [ematito_._gmail.com] > Try to write the checkpoint file (Fchk). Some the quantities that > are > written there have more > precision than in the standard outputs. Of course it will only help > if > the quantities you want > are included in the fchk too. I guess normal modes are included in > the > fchk. > > Otherwise I'm afraid you have to change the code and recompile. > > Eduard > > On Feb 1, 2011, at 10:38 PM, Leonid Shirkov leonid.shirkov!A! > tiger.chem.uw.edu.pl wrote: > > > > > Sent to CCL by: "Leonid Shirkov" [leonid.shirkov _ > > tiger.chem.uw.edu.pl] > > > > Dear Colleagues, > > > > I need to have more digits after the decimal point in the > Gaussian > > output. > > For example, when I do PES Scan and have the final table, there > are > > only five digits. Of course, I can > > find more precise values in the output file, but I thought maybe > > there is a way to define the precision > > in the final table. > > Another example is the eigenvectors in frequency analysis, by > > default they are printed with 2 digits. > > Thank you in advance! > > > > Regards, > > Leonid > > > > > > > > -= This is automatically added to each message by the mailing > script > > =- > > To recover the email address of the author of the message, please > > > change> Conferences: > http://server.ccl.net/chemistry/announcements/ > > conferences/> > > > > -- > Eduard Matito > Postdoctoral researcher > Institute of Physics > University of Szczecin > Wielkopolska 15 > 70451 Szczecin (Poland) > Phone: +48914441436 > http://ematito.webs.com > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the ++ sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Thu Feb 3 12:47:00 2011 From: "Christos E. Kefalidis kefalidi ~~ aol.com" To: CCL Subject: CCL:G: UV/VIS Gaussian09 Message-Id: <-43849-110203082438-29466-IsJaOMXxN1GVcr0xxUhiwA * server.ccl.net> X-Original-From: "Christos E. Kefalidis" Content-Type: multipart/alternative; boundary="--------MB_8CD91BCCA7BBC1A_11C0_16E6D_webmail-d055.sysops.aol.com" Date: Thu, 3 Feb 2011 08:24:16 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: "Christos E. Kefalidis" [kefalidi]*[aol.com] This is a multi-part message in MIME format. ----------MB_8CD91BCCA7BBC1A_11C0_16E6D_webmail-d055.sysops.aol.com Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Hi Krishna, This error is probably due to basis set linear dependency. Probably = the basis set you chose includes too many diffuse functions. You should = reduce it somehow, in order to get ride of this error. =20 Christos =20 =20 On 3/2/2011 07:38, Krishna Kuben Govender kk.govender^gmail.com wrot= e: =20 =20 Sent to CCL by: "Krishna Kuben Govender" [kk.govender^_^gmail.com] Good day everyone, I trust that there is someone who maybe able to aid me with a problem I am = having regarding the generation of UV/Vis spectra using Gaussian 09. I have fairly large Iron (Fe) system which I have successfully optimized an= d confirmed that it lies at a minima on the potential energy surface by gen= erating the Frequencies for this optimized molecule. I then took the above mentioned system and submitted it for a single point = time dependent simulation using the following input: # OPBE/ChkBasis NoSymm Guess=3DRead Geom=3Dallcheck TD(NState=3D5) The simulation runs for a short while, but then crashes out with the follow= ing warning and error, respectively: Warning: The smallest alpha delta epsilon is .... Fatal Problem: The smallest beta delta epsilon is .... Can anyone provide me with some solutions to my problem. I would really app= reciate any help with the matter, especially since this is the first time t= hat I am trying to carry out simulations of this nature. Thanks in advance for your help. Regards, Krishna Kuben Govender PhD Graduate Student University of Cape Town Scientific Computing Research Unit -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt=20 =20 =20 =20 --=20 ------------------------------------------------------------- Christos E. KEFALIDIS Institut Charles Gerhardt, Equipe Chimie Th=C3=A9orique, M=C3=A9thodologies, Mod=C3=A9lisations, Universit=C3=A9 Montpellier II, B=C3=A2t. 15, CC-1501, Place Eugene Bataillon, 34090 Montpellier Cedex5, FRANCE Tel : +33(0)4 67 14 36 52 Fax : +33(0)4 67 14 48 39 http://ctmm.icgm.fr/spip.php?rubrique91 =20 =20 ----------MB_8CD91BCCA7BBC1A_11C0_16E6D_webmail-d055.sysops.aol.com Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="utf-8"
=20 =20 Hi Krishna,
This error is probably due to basis set linear dependency. Probably the basis set you chose includes too many diffuse functions. You should reduce it somehow, in order to get ride of this error.

Christos


On 3/2/2011 07:38, Krishna Kuben Govender kk.govender^gmail.com wrote: 
Sent to CCL by: "Krishna Kuben Govender" [kk.govender^=
_^gmail.com]


Good day everyone,





I trust that there is someone who maybe able to aid me with a problem I am =
having regarding the generation of UV/Vis spectra using Gaussian 09.





I have fairly large Iron (Fe) system which I have successfully optimized an=
d confirmed that it lies at a minima on the potential energy surface by gen=
erating the Frequencies for this optimized molecule.





I then took the above mentioned system and submitted it for a single point =
time dependent simulation using the following input:





# OPBE/ChkBasis NoSymm Guess=3DRead Geom=3Dallcheck TD(NState=3D5)





The simulation runs for a short while, but then crashes out with the follow=
ing warning and error, respectively:


Warning: The smallest alpha delta epsilon is ....


Fatal Problem: The smallest beta delta epsilon is ....





Can anyone provide me with some solutions to my problem. I would really app=
reciate any help with the matter, especially since this is the first time t=
hat I am trying to carry out simulations of this nature.





Thanks in advance for your help.





Regards,


Krishna Kuben Govender


PhD Graduate Student


University of Cape Town


Scientific Computing Research Unit











-=3D This is automatically added to each message by the mailing script =3D-=





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-- 


-------------------------------------------------------------


Christos E. KEFALIDIS


Institut Charles Gerhardt,


Equipe Chimie Th=C3=A9orique, M=C3=A9thodologies, Mod=C3=A9lisations,


Universit=C3=A9 Montpellier II, B=C3=A2t. 15, CC-1501,


Place Eugene Bataillon,


34090 Montpellier Cedex5,


FRANCE





Tel :  +33(0)4 67 14 36 52


Fax : +33(0)4 67 14 48 39





http://ctmm.icgm.fr/spip.php?rubrique91
 ----------MB_8CD91BCCA7BBC1A_11C0_16E6D_webmail-d055.sysops.aol.com-- From owner-chemistry@ccl.net Thu Feb 3 13:22:00 2011 From: "Simone Kossmann simone[*]thch.uni-bonn.de" To: CCL Subject: CCL: paralell Jobs in ORCA using Grimme's functional mPW2PLYP Message-Id: <-43850-110203084238-25115-PPjiwcUKLGxX5BD/pmgNrQ-*-server.ccl.net> X-Original-From: Simone Kossmann Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 03 Feb 2011 14:42:30 +0100 MIME-Version: 1.0 Sent to CCL by: Simone Kossmann [simone{=}thch.uni-bonn.de] Dear Giovanni, your error couldn't be reproduced. Maybe you are using an old ORCA version? All the best, Simone From owner-chemistry@ccl.net Thu Feb 3 13:56:00 2011 From: "Geoff Skillman skillman---eyesopen.com" To: CCL Subject: CCL: Large .XYZ file visualization Message-Id: <-43851-110203125305-24528-8MzqK1nfpJreiHH4iB4Pzw++server.ccl.net> X-Original-From: Geoff Skillman Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 3 Feb 2011 09:51:22 -0800 MIME-Version: 1.0 Sent to CCL by: Geoff Skillman [skillman a eyesopen.com] Hi Alex- VIDA should be able to handle your task. As a test, I took the 3o8o.pdb structure of 6-Phosphofructokinase (46645 atoms) and saved it in .xyz format (no connection records). VIDA reads it in, perceives the bonds, residues and chains all in a couple seconds (desktop workstation hardware). It is available free for non-commercial academic use (www.eyesopen.com). Geoff Skillman OpenEye -----Original Message----- > From: owner-chemistry+skillman==eyesopen.com _ ccl.net [mailto:owner-chemistry+skillman==eyesopen.com _ ccl.net] On Behalf Of Marcel Swart marcel.swart###icrea.cat Sent: Thursday, February 03, 2011 5:22 AM To: Geoff Skillman Subject: CCL: Large .XYZ file visualization Sent to CCL by: Marcel Swart [marcel.swart=-=icrea.cat] Hi Alex, I think you should be careful, normally people use PDB files that contain not only the atomic coordinates, but also residue names and numbers; this makes the visualization of e.g. proteins quite easy using e.g. VMD, Rasmol, etc. This is in part also because the connection tables are known for most of the residues; in principle, if you just give the program xyz files with atomic coordinates, it has to find out these connections (which can be done, but may take some time). Marcel On Feb 3, 2011, at 11:29 AM, Alex Naden anaden===fsmail.net wrote: > Hello All, > > Thank you for your replies and suggestions. > > Just to expand on my original question: > > I am trying to look at the .xyz files containing 25000 of atoms and more. I have tried opening them in several freeware Lunux based programs before posting the question on the forum but without much success, as the structures were loaded for an indefinite length of time (well in excess of two hours). I am not sure whether it is partially to do with my machine spec (Intel Pentium 4, 1 Gb memory) or the inability of the programs that I have picked to handle this amount of atoms. Hence, was my question on the forum. > > I am going to try the suggested programs. > > Thank you all for your help. > > Alex From owner-chemistry@ccl.net Thu Feb 3 14:31:00 2011 From: "Manuel Melle Franco manuelmelle::gmail.com" To: CCL Subject: CCL: Building Nanoparticles Message-Id: <-43852-110203130235-32690-PO8CTpabol4ulIBys8l2QA..server.ccl.net> X-Original-From: Manuel Melle Franco Content-Type: multipart/alternative; boundary=0015175cf746a66141049b6491e5 Date: Thu, 3 Feb 2011 18:02:09 +0000 MIME-Version: 1.0 Sent to CCL by: Manuel Melle Franco [manuelmelle~!~gmail.com] --0015175cf746a66141049b6491e5 Content-Type: text/plain; charset=ISO-8859-1 Dear Edroaldo, I have never built a truncated octahedron but If I had to a couple of things come to mind: A truncated octahedron may seem quite difficult to build but at the end, it is not anything more than an octahedron with trucated points: http://en.wikipedia.org/wiki/Truncated_octahedron Basically you have to built an octahedron and then truncate it (cut the points). For this there are two easy choices: 1) you do it by hand with some graphical interface: For instance with Xmakemol, a nice but not updated anymore software, that allows you to rotate systems by specific angles and cut out rectaungular parts of it with the mouse... 2) you can do the same thing with some python/perl programming. regards Manuel ____________________________________________________________ Mohandas K. Gandhi often changed his mind publicly. An aide once asked him how he could so freely contradict this week what he had said just last week. The great man replied that it was because this week he knew better. ____________________________________________________________ Manuel Melle-Franco, Ph.D. Investigador Auxiliar do Requimte Theoretical and Computational Chemistry Group Chemistry Department Faculty of Sciences University of Porto Rua do Campo Alegre,687 4169-007 Porto Portugal. --------------------------------------------------------- A mind all logic is like a knife all blade. It makes the hand bleed that uses it. Rabindranath Tagore --------------------------------------------------------- On Tue, Feb 1, 2011 at 4:02 PM, Edroaldo Lummertz da Rocha edroaldo*o* gmail.com wrote: > > Sent to CCL by: "Edroaldo Lummertz da Rocha" [edroaldo:_:gmail.com] > Hi, I am starting to construct models to use in molecular dynamics > simulations and I can not find information about how build atomistic > nanoparticles and nanomaterials models. For example, I need to model a > truncated octahedron gold nanoparticle. What is the methodology for that? I > build the FCC unit cell and the periodic structure but I do not know how to > get a spherical morphology, for example. Could anyone give me a direction to > do that? Is there a free software? I read some previous messages here and I > found a post about Materials Studio. However I do not have access to > Materials Studio and I need free software or some methodology for that. Any > direction is useful. Thanks so much. > > Edroaldo Lummertz da Rocha > edroaldo---gmail.com> > > --0015175cf746a66141049b6491e5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Edroaldo,=A0


I have never b= uilt a truncated octahedron but If I had to a couple of things come to mind= :

A truncated octahedron may seem quite difficult to buil= d but at the end, it is not anything more than=A0
an octahedron w= ith trucated points:

http://en.wikipedia.org/wiki/Truncated_octahedr= on

Basically you have to built an octahedron and then truncate = it (cut the points).=A0

For this there are two eas= y choices:

1) you do it by hand with some graphica= l interface:

For instance with Xmakemol, a nice but not updated anym= ore software, =A0that allows you to rotate systems by specific angles and c= ut out rectaungular parts of it with the mouse...

2) you can do the same thing =A0with some python/perl programming.=A0
=

regards

Manuel

<= /div>

_______________________________________________= _____________

Mohandas K. Gandhi often changed his mind publicly.=A0 An aide once ask= ed
him how he could so freely contradict this week what he had said just=
last week.=A0 The great man replied that it was because this week he kn= ew
better.

____________________________________________________________=

Manuel Melle-Franco, Ph.D.
Investigador Auxiliar do Requimte Theoretical and Computational Chemistry Group
Chemistry Department
Faculty of Sciences
University of Porto
Rua do Campo Alegre,687
41= 69-007 Porto
Portugal.
----------------------------------------------= -----------

A mind all logic is like a knife all blade. It makes the= hand bleed that uses it.
Rabindranath Tagore

------------------------------------------------= ---------


On Tue, Feb 1, 2011 at 4:02 PM, Edroaldo= Lummertz da Rocha edroaldo*o*gmail.com <owner-chemis= try[a]ccl.net> wrote:

Sent to CCL by: "Edroaldo Lummertz =A0da Rocha" [edroaldo:_:gmail.com]
Hi, I am starting to construct models to use in molecular dynamics simulati= ons and I can not find information about how build atomistic nanoparticles = and nanomaterials models. For example, I need to model a truncated octahedr= on gold nanoparticle. What is the methodology for that? I build the FCC uni= t cell and the periodic structure but I do not know how to get a spherical = morphology, for example. Could anyone give me a direction to do that? Is th= ere a free software? I read some previous messages here and I found a post = about Materials Studio. However I do not have access to Materials Studio an= d I need free software or some methodology for that. Any direction is usefu= l. =A0Thanks so much.

Edroaldo Lummertz da Rocha
edroaldo---gmail.= com



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--0015175cf746a66141049b6491e5-- From owner-chemistry@ccl.net Thu Feb 3 15:06:00 2011 From: "James Womack james.c.womack(0)gmail.com" To: CCL Subject: CCL: Electron density over elliptic coordinates Message-Id: <-43853-110203103345-6244-Wb9BgJc06ZG7Ob9JBWct2Q===server.ccl.net> X-Original-From: James Womack Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 03 Feb 2011 15:19:12 +0000 MIME-Version: 1.0 Sent to CCL by: James Womack [james.c.womack ~ gmail.com] Hello, I am trying to work out how to evaluate the electron density for a two electron He-like, using a Hylleraas-type wavefunction based on elliptic coordinates (s=r1+r2, t=r1-r2, u=r12, where r1 and r2 are the distances of the 2 electrons from the nucleus and r12 is the interelectronic distance). I know the electronic density as a function of distance from the nucleus, r, can be represented using Dirac notation as < U | DiracDelta[r - r1] | U >, where U is the wavefunction, however I am unsure as to how to convert this integral over r1 and r2 into an integral over elliptic coordinates. Any help or suggestions would be greatly appreciated. Regards, James From owner-chemistry@ccl.net Thu Feb 3 16:40:00 2011 From: "Jiabo Li jiaboli..yahoo.com" To: CCL Subject: CCL: VB2000 for ICT Message-Id: <-43854-110203163853-24047-/JfyXly3izeHuSu+D+8JXA!=!server.ccl.net> X-Original-From: Jiabo Li Content-Type: multipart/alternative; boundary="0-563225523-1296769127=:96588" Date: Thu, 3 Feb 2011 13:38:47 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Jiabo Li [jiaboli#,#yahoo.com] --0-563225523-1296769127=:96588 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Peter, =A0 I had a quick look at your structure and your input. There are a few obviou= s error in your input. In your molecule,=A0there only=A015 atoms (instead o= f 16)=A0contribute 15 atomic pi orbitals. Second, in you VBSTR group, you p= ut 3 electrons on orbital 13, which is invalid.=20 =A0 Generally speaking, the most tricky part in any VB calculation is to specif= y the electron groups and the generation of the initial VB orbitals. The VB= 2000 team=A0has put considerable efforts to make this easier and apparently= there are still more=A0need to be done. VB2000 divides=A0electrons into=A0= different groups based on localized molecular orbitals (LMOs). In simple ca= se, VB2000 is=A0smart enough to do this automatically. However,=A0for most = interesting systems, like yours, you have to put extra efforts by looking t= he LMOs, and determining which LMO belongs to which group (in your case, si= gma group and pi group).=A0This can be done by using the keyword LMOGRPMODI= FY.=A0 =A0 For 16 electron VB group, you need download an additional auxiliary file fr= om the VB2000 website.=A0If you need additional help, you can contact Dr. B= rian Duke or me offline.=20 =A0 Jiabo=A0 --- On Wed, 2/2/11, P.D.Jarowski-x-surrey.ac.uk w= rote: > From: P.D.Jarowski-x-surrey.ac.uk Subject: CCL: VB2000 for ICT To: "Li, Jiabo " Date: Wednesday, February 2, 2011, 6:05 AM Dear All. I am new to valence-bond theory. I have started to implement VB2000 to look= into some valence-bond structures of a common intramolecular charge transf= er organic molecule. I am having great difficulty understanding how to cons= truct the valence structures using multi-structure VB as implemented in VB2= 000. =A0I am trying to represent the ground state and the most important ic= t structure where a negative charge resides on a dicyanomethilidine and the= positive charge on the dimethylammonium. =A0(you may need to load the stru= cture to understand) Am I even close? What other keywords will I need? Do I= need to use Group Function Theory here? Any help would be much appreciated= . Thanks a lot, Peter Here is my input file: #! VB(16)/sto-3g PRINTALL Multi-structure VB on parent ICT 0 1 =A06 =A0=A0=A0=A03.563680 =A0=A0=A0=A01.141199 =A0=A0=A0-0.572289 =A06 =A0=A0=A0=A02.621660 =A0=A0=A0=A01.846249 =A0=A0=A0=A00.219742 =A06 =A0=A0=A0=A01.353289 =A0=A0=A0=A01.336271 =A0=A0=A0=A00.431174 =A06 =A0=A0=A0=A00.933208 =A0=A0=A0=A00.106721 =A0=A0=A0-0.120267 =A06 =A0=A0=A0=A01.876447 =A0=A0=A0-0.591072 =A0=A0=A0-0.908703 =A06 =A0=A0=A0=A03.146954 =A0=A0=A0-0.098015 =A0=A0=A0-1.130923 =A06 =A0=A0=A0-0.403269 =A0=A0=A0-0.369136 =A0=A0=A0=A00.138772 =A06 =A0=A0=A0-0.984818 =A0=A0=A0-1.523489 =A0=A0=A0-0.303534 =A06 =A0=A0=A0-2.323381 =A0=A0=A0-1.863636 =A0=A0=A0=A00.035966 =A06 =A0=A0=A0-2.991754 =A0=A0=A0-2.999993 =A0=A0=A0-0.360778 =A06 =A0=A0=A0-4.341113 =A0=A0=A0-3.234581 =A0=A0=A0=A00.044904 =A07 =A0=A0=A0-5.441353 =A0=A0=A0-3.415245 =A0=A0=A0=A00.381893 =A07 =A0=A0=A0=A04.827129 =A0=A0=A0=A01.632924 =A0=A0=A0-0.792194 =A06 =A0=A0=A0=A05.772546 =A0=A0=A0=A00.887686 =A0=A0=A0-1.610742 =A06 =A0=A0=A0-2.368274 =A0=A0=A0-3.984922 =A0=A0=A0-1.188824 =A07 =A0=A0=A0-1.835295 =A0=A0=A0-4.770468 =A0=A0=A0-1.863661 =A06 =A0=A0=A0=A05.229343 =A0=A0=A0=A02.903781 =A0=A0=A0-0.208745 =A01 =A0=A0=A0=A00.656231 =A0=A0=A0=A01.903617 =A0=A0=A0=A01.043960 =A01 =A0=A0=A0=A01.607515 =A0=A0=A0-1.542408 =A0=A0=A0-1.358036 =A01 =A0=A0=A0=A02.885525 =A0=A0=A0=A02.795444 =A0=A0=A0=A00.669595 =A01 =A0=A0=A0=A03.828262 =A0=A0=A0-0.675645 =A0=A0=A0-1.743500 =A01 =A0=A0=A0-2.876313 =A0=A0=A0-1.169192 =A0=A0=A0=A00.665391 =A01 =A0=A0=A0=A04.598596 =A0=A0=A0=A03.730733 =A0=A0=A0-0.562224 =A01 =A0=A0=A0=A05.179834 =A0=A0=A0=A02.880541 =A0=A0=A0=A00.888333 =A01 =A0=A0=A0=A06.259438 =A0=A0=A0=A03.119340 =A0=A0=A0-0.495099 =A01 =A0=A0=A0=A05.985874 =A0=A0=A0-0.102260 =A0=A0=A0-1.185661 =A01 =A0=A0=A0=A05.401103 =A0=A0=A0=A00.747629 =A0=A0=A0-2.634749 =A01 =A0=A0=A0=A06.711133 =A0=A0=A0=A01.440397 =A0=A0=A0-1.665373 =A01 =A0=A0=A0-1.011991 =A0=A0=A0=A00.283540 =A0=A0=A0=A00.766208 =A01 =A0=A0=A0-0.434020 =A0=A0=A0-2.218369 =A0=A0=A0-0.932359 $02PIVBO 16 1,2,3,4,5,6,7,8,9,10,11,12,13,15,16 $02VBSTR 4 1 2 3 4 5 6 7 8 9 10 11 12 13 13 14 15 1 13 13 13 2 3 4 7 5 6 8 9 10 10 11 12 14 15 --0-563225523-1296769127=:96588 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Peter,
 
I had a quick look at your structure and your input. There are a few o= bvious error in your input. In your molecule, there only 15 atoms= (instead of 16) contribute 15 atomic pi orbitals. Second, in you VBST= R group, you put 3 electrons on orbital 13, which is invalid.
 
Generally speaking, the most tricky part in any VB calculation is to s= pecify the electron groups and the generation of the initial VB orbitals. T= he VB2000 team has put considerable efforts to make this easier and ap= parently there are still more need to be done. VB2000 divides ele= ctrons into different groups based on localized molecular orbitals (LM= Os). In simple case, VB2000 is smart enough to do this automatically. = However, for most interesting systems, like yours, you have to put ext= ra efforts by looking the LMOs, and determining which LMO belongs to which = group (in your case, sigma group and pi group). This can be done by us= ing the keyword LMOGRPMODIFY. 
 
For 16 electron VB group, you need download an additional auxiliary fi= le from the VB2000 website. If you need additional help, you can conta= ct Dr. Brian Duke or me offline.
 
Jiabo 

--- On Wed, 2/2/11, P.D.Jarowski-x-surrey.ac.uk = <owner-chemistry|,|ccl.net> wrote:

From: P.D.Jarowski-x-surrey.ac.uk <owner-chemi= stry|,|ccl.net>
Subject: CCL: VB2000 for ICT
To: "Li, J= iabo " <jiaboli|,|yahoo.com>
Date: Wednesday, February 2, 20= 11, 6:05 AM

<= SPAN style=3D"FONT-SIZE: 11pt">Dear All.

I am new to valence-bond th= eory. I have started to implement VB2000 to look into some valence-bond str= uctures of a common intramolecular charge transfer organic molecule. I am h= aving great difficulty understanding how to construct the valence structure= s using multi-structure VB as implemented in VB2000.  I am trying to r= epresent the ground state and the most important ict structure where a nega= tive charge resides on a dicyanomethilidine and the positive charge on the = dimethylammonium.  (you may need to load the structure to understand) = Am I even close? What other keywords will I need? Do I need to use Group Fu= nction Theory here? Any help would be much appreciated.

Thanks a lot= ,

Peter

Here is my input file:

#= ! VB(16)/sto-3g PRINTALL

Multi-structure VB on parent ICT

0 1<= BR> 6     3.563680     1.14119= 9    -0.572289
 6     2.621660 &= nbsp;   1.846249     0.219742
 6=     1.353289     1.336271  &n= bsp;  0.431174
 6     0.933208  =    0.106721    -0.120267
 6  &nb= sp;  1.876447    -0.591072    -0.90= 8703
 6     3.146954    -0.09801= 5    -1.130923
 6    -0.403269  =   -0.369136     0.138772
 6  &nb= sp; -0.984818    -1.523489    -0.303534<= BR> 6    -2.323381    -1.863636     0.035966
 6    -2.991754 &n= bsp;  -2.999993    -0.360778
 6  &nbs= p; -4.341113    -3.234581     0.044= 904
 7    -5.441353    -3.415245 &nbs= p;   0.381893
 7     4.827129 &n= bsp;   1.632924    -0.792194
 6  = ;   5.772546     0.887686   &n= bsp;-1.610742
 6    -2.368274    -3.9= 84922    -1.188824
 7    -1.835295 &n= bsp;  -4.770468    -1.863661
 6  &nbs= p;  5.229343     2.903781    -= 0.208745
 1     0.656231    &nbs= p;1.903617     1.043960
 1     1.607515    -1.542408   &= nbsp;-1.358036
 1     2.885525   &nbs= p; 2.795444     0.669595
 1   &n= bsp; 3.828262    -0.675645    -1.743500<= BR> 1    -2.876313    -1.169192  &n= bsp;  0.665391
 1     4.598596  =    3.730733    -0.562224
 1  &nb= sp;  5.179834     2.880541    =  0.888333
 1     6.259438   &nbs= p; 3.119340    -0.495099
 1    &= nbsp;5.985874    -0.102260    -1.185661
&n= bsp;1     5.401103     0.747629 &nb= sp;  -2.634749
 1     6.711133     1.440397    -1.665373
 1 &n= bsp;  -1.011991     0.283540   &nbs= p; 0.766208
 1    -0.434020    -= 2.218369    -0.932359

$02PIVBO
16
1,2,3,4,5,6,7= ,8,9,10,11,12,13,15,16

$02VBSTR
4
1 2 3 4 5 6 7 8 9 10 11 12 1= 3 13 14 15
1 13 13 13 2 3 4 7 5 6 8 9 10 10 11 12 14 15
--0-563225523-1296769127=:96588-- From owner-chemistry@ccl.net Thu Feb 3 17:15:00 2011 From: "Mihaly Mezei Mihaly.Mezei]*[mssm.edu" To: CCL Subject: CCL: Truncated octahedron Message-Id: <-43855-110203164030-26890-Tixf4Kam84fPqpXBXzr6kg++server.ccl.net> X-Original-From: Mihaly Mezei Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Thu, 03 Feb 2011 16:40:24 -0500 MIME-version: 1.0 Sent to CCL by: Mihaly Mezei [Mihaly.Mezei-*-mssm.edu] > Sent to CCL by: "Edroaldo Lummertz da Rocha" [edroaldo:_:gmail.com] > Hi, I am starting to construct models to use in molecular dynamics > simulations and I can not find information about how build atomistic > nanoparticles and nanomaterials models. For example, I need to model a > truncated octahedron gold nanoparticle. What is the methodology > for that? My program Simulaid (http://inka.mssm.edu/~mezei/simulaid) can trim a set of atoms/molecules to be contained withi a number of periodic cell shapes, including truncated octehedron. It can also print a PDB file with the vertices of these shapes for easy visualization. Mihaly Mezei Department of Structural and Chemical Biology, Mount Sinai School of Medicine Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://atlas.physbio.mssm.edu From owner-chemistry@ccl.net Thu Feb 3 17:54:00 2011 From: "Lukman Olawale Olasunkanmi waleolasunkanmi===gmail.com" To: CCL Subject: CCL: dissenting results Message-Id: <-43856-110203171906-4569-ntvk4sX+U8Gi8D2ZbVlWYw a server.ccl.net> X-Original-From: Lukman Olawale Olasunkanmi Content-Type: multipart/alternative; boundary=00163683340ae96039049b68265e Date: Thu, 3 Feb 2011 22:18:58 +0000 MIME-Version: 1.0 Sent to CCL by: Lukman Olawale Olasunkanmi [waleolasunkanmi.:.gmail.com] --00163683340ae96039049b68265e Content-Type: text/plain; charset=ISO-8859-1 Thank you. Here are typical results: After geometry optimization without any special keyword: FINAL HEAT OF FORMATION = 40.08240 KCAL/MOL With keyword "thermo", and LET GNORM = 109.40376 HEAT OF FORMATION = 43.366029 KCALS/MOLE Sometimes the difference may be up to 10kcal/mol for some calculations. Kindly give me an advice on it. thanks. wrote: > > Sent to CCL by: "Close, David M." [CLOSED!A!mail.etsu.edu] > This is very interesting. But you need to tell us how much the numbers > differ. I can see how sometimes very small difference could arise from > coding errors arising from one subroutine using a double precision variable, > and another subroutine using the same variable with a different word-length. > But these would be very small differences. Give us an example of how big > the differences are, and what keywords are used to control the accuracy of > each SCF cycle. > Regards, Dave Close. > > -----Original Message----- > > From: owner-chemistry+closed==etsu.edu-$-ccl.net [mailto: > owner-chemistry+closed ==etsu.edu-$-ccl.net] On > Behalf Of Lukman Olawale Olasunkanm waleolasunkanmi:gmail.com > Sent: Tuesday, February 01, 2011 8:43 AM > To: Close, David M. > Subject: CCL: dissenting results > > > Sent to CCL by: "Lukman Olawale Olasunkanm" [waleolasunkanmi#,#gmail.com] > Hello everyone, > I usually run my MOPAC job twice: first for ordinary optimization from > which I normally get the GNORM value ( and H.O.F., dipole moments, > HOMO-LUMO, COSMOS Area and volume etc.), and second for the thermo values > (with the specified value of the GNORM using the LET keyword). I discovered > that the values got for the common parameters like H.O.F, dipole moments > etc. in both cases differ. > What can you advise me to do please? > Thank youhttp:// > www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > -- *Olasunkanmi Lukman Olawale* *Department of Chemistry, Obafemi Awolowo University, Ile-Ife, Nigeria.* *+234-08052401564* *"Improving our own attitudes and our own state of mind takes time. Haste and impatience can only defeat our purposes."* --00163683340ae96039049b68265e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thank you.
Here are typical results:
After geometry optimization with= out any special keyword:
FINAL HEAT OF FORMATION =3D=A0 40.08240 KCAL/MO= L

With keyword "thermo", and LET GNORM =3D 109.40376
<= br> HEAT OF FORMATION =3D=A0=A0=A0=A0=A0 43.366029 KCALS/MOLE

Sometimes = the difference may be up to 10kcal/mol for some calculations.
Kindly gi= ve me an advice on it.
thanks.


wrote:

Sent to CCL by: "Close, David M." [CLOSED!A!mail.etsu.edu]
This is very interesting. =A0But you need to tell us how much the numbers d= iffer. =A0I can see how sometimes very small difference could arise from co= ding errors arising from one subroutine using a double precision variable, = and another subroutine using the same variable with a different word-length= . =A0But these would be very small differences. =A0Give us an example of ho= w big the differences are, and what keywords are used to control the accura= cy of each SCF cycle.
=A0Regards, 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 Lukman Olawale Olasunkanm w= aleolasunkanmi:gmail.com=
Sent: Tuesday, February 01, 2011 8:43 AM
To: Close, David M.
Subject: CCL: dissenting results


Sent to CCL by: "Lukman Olawale Olasunkanm" [waleolasunkanmi#,#gmail.com]
Hello everyone,
I usually run my MOPAC job twice: first for ordinary optimization from whic= h I normally get the GNORM value ( and H.O.F., dipole moments, HOMO-LUMO, C= OSMOS Area and volume etc.), and second for the thermo values (with the spe= cified value of the GNORM using the LET keyword). I discovered that the val= ues got for the common parameters like H.O.F, dipole moments etc. in both c= ases differ.
What can you advise me to do please?
Thank youhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.n= et/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt


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--
Olasunkanmi Lukman O= lawale

Department = of Chemistry,
Obafemi Awolowo University,
Ile-Ife, Nigeria.
= +234-08052401564

"Improving our own attitudes and our own state of mind ta= kes time. Haste and impatience can only defeat our purposes."

--00163683340ae96039049b68265e-- From owner-chemistry@ccl.net Thu Feb 3 18:29:00 2011 From: "Lukman Olawale Olasunkanmi waleolasunkanmi/a\gmail.com" To: CCL Subject: CCL: Organometallic builder Message-Id: <-43857-110203175641-28985-FZMx+Dlyw4Wie/JMqjjZWw(-)server.ccl.net> X-Original-From: Lukman Olawale Olasunkanmi Content-Type: multipart/alternative; boundary=000e0ce001326ae46c049b68adea Date: Thu, 3 Feb 2011 22:56:35 +0000 MIME-Version: 1.0 Sent to CCL by: Lukman Olawale Olasunkanmi [waleolasunkanmi**gmail.com] --000e0ce001326ae46c049b68adea Content-Type: text/plain; charset=ISO-8859-1 Dear All, Does anyone know of a free molecular builder that is very good at building organometallic compounds and it is windows compatible? Thank you -- *Olasunkanmi Lukman Olawale* *Department of Chemistry, Obafemi Awolowo University, Ile-Ife, Nigeria.* *+234-08052401564* *"Improving our own attitudes and our own state of mind takes time. Haste and impatience can only defeat our purposes."* --000e0ce001326ae46c049b68adea Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All,
Does anyone know of a free molecular builder that is very good= at building organometallic compounds and it is windows compatible?
Than= k you

--
Olasunkanmi Lukman Olawale

Department of Chemistry,
Obafemi Awolowo University,
Ile-Ife, Nigeria.
= +234-08052401564

"Improving our own attitudes and our own state of mind ta= kes time. Haste and impatience can only defeat our purposes."

--000e0ce001326ae46c049b68adea-- From owner-chemistry@ccl.net Thu Feb 3 22:33:00 2011 From: "=?GB2312?B?0vO9oQ==?= janeyin600=-=gmail.com" To: CCL Subject: CCL:G: Cannot generate a .cub file with G03 Message-Id: <-43858-110203223136-20865-B3Uk0F94odfmehEVJdXY9g#,#server.ccl.net> X-Original-From: =?GB2312?B?0vO9oQ==?= Content-Type: multipart/alternative; boundary=0016e64761da605bc5049b6c848b Date: Thu, 3 Feb 2011 21:31:26 -0600 MIME-Version: 1.0 Sent to CCL by: =?GB2312?B?0vO9oQ==?= [janeyin600!^!gmail.com] --0016e64761da605bc5049b6c848b Content-Type: text/plain; charset=GB2312 Content-Transfer-Encoding: quoted-printable Yes, it works very well! I replaced "density=3Dscf" with "spin=3DQCI", then I obtained the spin distribution right away. Thank you very much, Cheri! 2011/2/1 Cheri McFerrin cmcfer1^-^tigers.lsu.edu > hi jane: > > here is what i would do. run a single point energy using > qcisd(full)/6-31g*. > > afterwards, run this command in order to convert your .chk file to a .fch= k > file > > formchk file.chk file.fchk > > next, run this command to generate a .cube file > > cubegen 0 density=3Dscf file.fchk 0 h > > more, on formchk and cubegen and be found at gaussian.com > >>keywords>>gaussian09utilities > > the cubegen and formchk utilities will be the same for G03. > > hope this helps!! > > cheri > > 2011/2/1 =D2=F3=BD=A1 janeyin600|*|gmail.com > > Hello there, >> >> I am trying to generate a cube file with Gaussian03. However, every time >> it stops at a certain place. My command line is : >> *# QCISD(full)/6-31G* density=3Dcurrent cube=3D(spin,coarse)* >> with everything else and ***.cub in the end. >> >> And this is the ending of my output: >> >> Evaluate density. >> >> Using the spin density. >> >> Map the density over a grid of points, CutOff=3D 1.00D-06 >> >> Writing cube to file ***.cub. >> >> IGUnit=3D -31 Origin=3D -6.040794 -5.152992 -3.695616 >> >> N1=3D 72 XYZInc=3D 0.176392 0.000000 0.000000 >> >> N2=3D 61 XYZInc=3D 0.000000 0.176392 0.000000 >> >> N3=3D 42 XYZInc=3D 0.000000 0.000000 0.176392 >> >> I am pretty sure that it's not due to time running out and it just comes >> to a abrupt stop. I just wonder if anyone has the similar experience on = this >> and a solution at hand. Thank you very much! >> >> Jane >> > > --0016e64761da605bc5049b6c848b Content-Type: text/html; charset=GB2312 Content-Transfer-Encoding: quoted-printable
Yes, it works very well! I replaced "density=3Dscf" wit= h "spin=3DQCI", then I obtained the spin distribution right = away. Thank you very much, Cheri!

2011/2/1 Cheri McFerrin cmcfer1^-^tigers.lsu.edu <owner-chemistry ~ ccl.net>
hi jane:=20

here is what i would do.  run a single point energy using qcisd(f= ull)/6-31g*.

afterwards, run this command in order to convert your .chk file to a .= fchk file

formchk file.chk file.fchk

next, run this command to generate a .cube file

cubegen 0 density=3Dscf file.fchk 0 h

more, on formchk and cubegen and be found at gaussian.com>>keywords>>gaussian0= 9utilities

the cubegen and formchk utilities will be the same for G03.

hope this helps!!

cheri

2011/2/1 =D2=F3=BD=A1 janeyin600|*|gmail.com <owner-chemistry**= ccl.net>=20

Hello there,
 
I am trying to generate a cube file with Gaussian03. However, every ti= me it stops at a certain place. My command line is :
# QCISD(full)/6-31G*= density=3Dcurrent cube=3D(spin,coarse)
with everything else and ***.cub in the end.<= /div>

And this is the ending of my output:

Evaluate density.

Using the spin density.

Map the density over a grid of points, CutOff=3D= 1.00D-06

Writing cube to file ***.cub.

IGUnit=3D -31 Origin=3D -6.040794 -5.152992 -3.6= 95616

N1=3D 72 XYZInc=3D 0.176392 0.000000 0.000000

N2=3D 61 XYZInc=3D 0.000000 0.176392 0.000000

N3=3D 42 XYZInc=3D 0.000000 0.000000 0.176392

I am pretty sure that it's not due to time r= unning out and it just comes to a abrupt stop. I just wonder if anyone has = the similar experience on this and a solution at hand. Thank= you very much!

Jane 



--0016e64761da605bc5049b6c848b-- From owner-chemistry@ccl.net Thu Feb 3 23:07:00 2011 From: "Jing Kong jkong[]q-chem.com" To: CCL Subject: CCL: Reminder: Workshop on Electronic Structure Calculations Message-Id: <-43859-110203175027-23779-yF4m9TLwGTVxRbUYOvFdsw/./server.ccl.net> X-Original-From: "Jing Kong" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_001B_01CBC3CA.C91B49D0" Date: Thu, 3 Feb 2011 17:50:02 -0500 MIME-Version: 1.0 Sent to CCL by: "Jing Kong" [jkong:-:q-chem.com] This is a multi-part message in MIME format. ------=_NextPart_000_001B_01CBC3CA.C91B49D0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear Colleague, This is a reminder that Q-Chem will hold a workshop on electronic structure calculations. It will consist of seminars by several leading quantum chemists and hands-on tutorials, and will highlight the much anticipated release of Q-Chem 4.0. The one-day workshop will take place on Saturday, March 26 in Anaheim, CA, right before the National ACS Meeting. We offer free six-month licenses of unlimited use of Q-Chem 4.0 for the workshop participants. The registration deadline is Feb 28. Please visit the workshop webpage (http://www.q-chem.com/wslal_hh.html) for registration and other details. Included below is the first announcement. I apologize if you receive multiple copies of this message. Happy Computing! Jing Kong **** Jing Kong, Ph.D., CEO & Chief Scientist, Q-Chem Inc. (http://www.q-chem.com) -----Original Message----- > From: Jing Kong [mailto:jkong . q-chem.com] Sent: Tuesday, January 04, 2011 3:21 PM To: 'chemistry . ccl.net' Subject: Workshop on Electronic Structure Calculations in Conjunction with Anaheim ACS Dear Colleague: Q-Chem Inc. would like to invite you to a workshop on Saturday, March 26, preceding the national ACS meeting in Anaheim and highlighting the release of the Q-Chem 4.0 software package. Q-Chem 4.0 contains significant new functionality, including: * TD-DFT gradient for excited-state structure optimization; * IRC searches for mapping complicated potential energy surfaces; * Range-separated and dispersion-corrected DFT functionals; * Faster algorithms for DFT, HF and coupled-cluster calculations; * More choices for excited-state, solvation and charge-transfer calculations; * Effective Fragment Potential and QM/MM for treating large systems; * Maximum Overlap Method for excited-state calculations of large systems; * Intracules for analysis of two-electron properties; * Shared-memory for multicore systems and implementations for GPUs; as well as many other areas. The workshop will consist of seminars and hands-on tutorials. Seminar speakers include Martin Head-Gordon (Berkeley), Peter Gill (ANU), Anna Krylov (USC), John Herbert (Ohio State), Paul Ha-Yeon Cheong (Oregon State) and Jing Kong (Q-Chem). Tutorials will be run by Yihan Shao and Zhengting Gan from Q-Chem, Inc. The meeting takes place from 8:30 a.m. to 4:30 p.m. at Doubletree Guest Suites Anaheim Resort/Convention Center (2085 S. Harbor Boulevard, Anaheim, CA 92802). The registration fee is $50 and covers continental breakfast, lunch, coffee and soft drinks. Please register by February 28 on our website (http://www.q-chem.com/wslal_hh.html) and bring your laptop (Windows 7/Vista/XP or Mac) for the tutorials. The software and tutorial materials will be available for downloading on the website after March 12. All workshop participants will receive a free six-month license for unlimited use of Q-Chem 4.0. I apologize if you receive multiple copies of this announcement. Happy New Year, Jing Kong, PhD CEO and Chief Scientist Q-Chem, Inc. ------=_NextPart_000_001B_01CBC3CA.C91B49D0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear = Colleague,

 

This is a reminder that Q-Chem will hold a workshop = on electronic structure calculations.  It will consist of seminars = by several leading quantum chemists and hands-on tutorials, and will = highlight the much anticipated release of Q-Chem 4.0. The one-day = workshop will take place on Saturday, March 26 in Anaheim, CA, right = before the National ACS Meeting. We offer free six-month licenses of = unlimited use of Q-Chem 4.0 for the workshop participants. The = registration deadline is Feb 28.  Please visit the workshop webpage = (http://www.q-chem.com/wslal_= hh.html) for registration and other details.  Included below is = the first announcement.

 

I = apologize if you receive multiple copies of this = message.

 

Happy Computing!

 

Jing = Kong

 

****

Jing = Kong, Ph.D., CEO & Chief Scientist, Q-Chem Inc. (http://www.q-chem.com)

<= p class=3DMsoPlainText> 

 

-----Original Message-----

From: Jing Kong [mailto:jkong . q-chem.com] =

Sent: Tuesday, January 04, 2011 = 3:21 PM

To: = 'chemistry . ccl.net'

Subject: = Workshop on Electronic Structure Calculations in Conjunction with = Anaheim ACS

 

Dear = Colleague:

 

Q-Chem Inc. would like to invite you to a workshop = on Saturday, March 26, preceding the national ACS meeting in Anaheim and = highlighting the release of the Q-Chem 4.0 software package.  = Q-Chem 4.0 contains significant new functionality, = including:

 

* TD-DFT gradient for excited-state structure = optimization;

* IRC searches for = mapping complicated potential energy surfaces;

* Range-separated and dispersion-corrected DFT = functionals;

* Faster algorithms = for DFT, HF and coupled-cluster calculations;

* More choices for excited-state, solvation and = charge-transfer calculations;

* = Effective Fragment Potential and QM/MM for treating large = systems;

* Maximum Overlap Method = for excited-state calculations of large systems;

* Intracules for analysis of two-electron = properties;

* Shared-memory for = multicore systems and implementations for GPUs; as well as many other = areas.

 

The workshop will consist of seminars and hands-on = tutorials.  Seminar speakers include Martin Head-Gordon (Berkeley), = Peter Gill (ANU), Anna Krylov (USC), John Herbert (Ohio State), Paul = Ha-Yeon Cheong (Oregon State) and Jing Kong (Q-Chem).  Tutorials = will be run by Yihan Shao and Zhengting Gan from Q-Chem, = Inc.

The meeting takes place from = 8:30 a.m. to 4:30 p.m. at Doubletree Guest Suites Anaheim = Resort/Convention Center (2085 S. Harbor Boulevard, Anaheim, CA = 92802).  The registration fee is $50 and covers continental = breakfast, lunch, coffee and soft drinks. 

 

Please = register by February 28 on our website = (http://www.q-chem.com/wslal_hh.html) and bring your laptop (Windows = 7/Vista/XP or Mac) for the tutorials.   The software and = tutorial materials will be available for downloading on the website = after March 12.

 

 

 

All = workshop participants will receive a free six-month =  license for unlimited use of Q-Chem 4.0.

I apologize if you receive multiple copies of this = announcement.

 

Happy = New Year,

 

Jing Kong, PhD

CEO and Chief Scientist

Q-Chem, Inc.

 

 

------=_NextPart_000_001B_01CBC3CA.C91B49D0--