From owner-chemistry@ccl.net Tue May 17 02:56:01 2011 From: "Serge Lavilier m.o.m-*-live.fr" To: CCL Subject: CCL:G: KEYWORD FOR PED CALCULATION Message-Id: <-44664-110517025519-21987-+m1ecpn6xlSAAH9JpGHqwA..server.ccl.net> X-Original-From: "Serge Lavilier" Date: Tue, 17 May 2011 02:55:16 -0400 Sent to CCL by: "Serge Lavilier" [m.o.m%x%live.fr] Hi, I want to do PED calculation with gaussian, and i search wich command i can do this. Best regards From owner-chemistry@ccl.net Tue May 17 04:12:00 2011 From: "Serdar Badoglu sbadoglu^^gazi.edu.tr" To: CCL Subject: CCL: stability and dipole moment Message-Id: <-44665-110517040625-26629-om6U+3TMoL0jyI7yPy4jfg+*+server.ccl.net> X-Original-From: "Serdar Badoglu" Date: Tue, 17 May 2011 04:06:21 -0400 Sent to CCL by: "Serdar Badoglu" [sbadoglu::gazi.edu.tr] Dear CCL'ers, I know that compounds with higher dipole moment posess lower stability. I'm looking for a good source (preferably a textbook) for an explanation. Any suggestions? From owner-chemistry@ccl.net Tue May 17 04:47:01 2011 From: "Serdar Bado?lu sbadoglu:_:gazi.edu.tr" To: CCL Subject: CCL:G: KEYWORD FOR PED CALCULATION Message-Id: <-44666-110517041134-28421-yglsWpol044Hqvb4SsgMYA(a)server.ccl.net> X-Original-From: "Serdar Bado?lu" Content-Type: text/plain; charset="iso-8859-9" Date: Tue, 17 May 2011 08:03:14 -0000 Sent to CCL by: "Serdar Bado?lu" [sbadoglu|a|gazi.edu.tr] On Tue, Mayŭs 17, 2011, "Serge Lavilier m.o.m-*-live.fr" dedi: As far as I know, Gaussian can't do PED calculations. You just need to have a software which can do PED/TED calculations. Those kind of software can generate PED/TED values by using your "frequency" calculations carried out by Gaussian. > > Sent to CCL by: "Serge Lavilier" [m.o.m%x%live.fr] > Hi, > I want to do PED calculation with gaussian, and i search wich command i can do this. > Best regards> > > -- Serdar BADOGLU Gazi University Department of Physics From owner-chemistry@ccl.net Tue May 17 05:21:00 2011 From: "vandestreek/a\avmatsim.de" To: CCL Subject: CCL: Tool to autocorrect hydrogen-positions from xray-structures? Message-Id: <-44667-110517045052-24131-vNSa7DCgudEa2QpaN1J7LQ.@.server.ccl.net> X-Original-From: vandestreek[]avmatsim.de Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Tue, 17 May 2011 10:50:18 +0200 MIME-Version: 1.0 Sent to CCL by: vandestreek=-=avmatsim.de Quoting "Guntram Schmidt guntram.schmidt(-)chemie.uni-halle.de" : > as it is well established, the bond length of light elements in > crystal structures are shortened due to effects like libration. (And more importantly for C-H, N-H and O-H, the H-peak in the electron density is shifted towards the heavier element, and X-rays measure the electron density, not the position of the nuclei.) > Is there any tool, to correct these bond length to "real" values, > especially for hydrogen atoms? The following paper appears relevant: http://scripts.iucr.org/cgi-bin/paper?so5037 but you are asking for a tool. I am sure there is software from / at the Cambridge Crystallographic Data Centre (CCDC) that does this (the authors of the paper above work there), but I do not know if it is available, and if it is, if it requires a subscription to their organic crystal structure database (the Cambridge Structural Database, CSD). I think the functionality you are looking for is in Mercury, but only in the commercial version, which requires a CSD license. Mercury is available on multiple platforms. Your affiliation is a German university, so I am pretty sure your university has a license. In that case, you can simply contact CCDC support: support(0)ccdc.cam.ac.uk they should be able to help you. I guess that PLATON is also able to do this: http://www.cryst.chem.uu.nl/platon/ I am pretty sure it is free and available for multiple platforms. Best wishes, -- Dr Jacco van de Streek Senior Scientist Avant-garde Materials Simulation Freiburg im Breisgau, Germany From owner-chemistry@ccl.net Tue May 17 05:57:00 2011 From: "Amrita Kumari amrita.g13 * gmail.com" To: CCL Subject: CCL: TINKER reg. Message-Id: <-44668-110517051950-20845-mKI274xTM/GlE+JF9f3mZA^server.ccl.net> X-Original-From: Amrita Kumari Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 17 May 2011 14:49:42 +0530 MIME-Version: 1.0 Sent to CCL by: Amrita Kumari [amrita.g13],[gmail.com] Dear Sir, Thankyou for your suggestion but I am not getting any folder like bin inside tinker directory which will have command to make .arc file. I have downloaded and installed VMD. so now visualization is not an issue but the main thing I am not getting is how can I make one file which will have dynamics of the molecule. On Sat, May 14, 2011 at 11:23 PM, Arun Kumar Subramanian wrote: > Hi > It seems that different people use different appendices like ".run", etc. > Even I have seen some combining all parameter commands with some other > files, that means its the commands that matters. > If you want to make .arc files the module for converting it is inside your > bin directory. You need to run interactively and answer all the question > that its gonna ask like what is the numbering and names of the first file in > the sequence and the last file and the interval etc. Then it will combine > all the .xyz files and return you a trajectory. I used VMD to view it. I am > not sure if Pymol can be used to view it in .arc format. Try to convert the > trajectory into a .pdb format, if you are successful, then you can easily > view it in pymol. Again, Pymol has a set of rules for the PDB nomenclature, > if that is missed, still it will show you the protein in line format. But if > you wanna view in cartoon, you should address this issue. I atleast know > that the VMD should be able to view it as a movie. I hope this helps you > currently. > regards, > ArunKumar. S. > > > > On Sat, May 14, 2011 at 5:12 AM, Amrita Kumari wrote: >> >> Dear Sir, >> >> Thankyou very much for your help. It has worked, I used .xyz input >> files from test directory and used the command given in .run file to >> test installation of TINKER and it has given the same result as >> whatsoever is there in .log file. Now one thing I am not getting that >> is how to visualize the output of Molecular Dynamics program. Like >> input .xyz file I am able to open in pymol but if I am using DYNAMICS >> program then how to visualize its output as a movie in pymol. what >> should be the format of output file and how to get it. I have read in >> TINKER manual that: Coordinate sets along the trajectory can be saved >> as sequentially numbered cycle files or directly to a TINKER archive >> .arc file. But I don't know how to get output as .arc file and how to >> visualize it as movie. Basically my aim is to use this software for >> some MD calculation and visualize the dynamics as movie. >> >> Thanks >> Amrita kumari >> Research Scholar >> IISER Mohali >> Chandigarh (INDIA). >> >> >> >> >> On Sat, May 14, 2011 at 5:58 AM, Arun Kumar Subramanian >> wrote: >> > hi >> > If you are a beginner to tinker and probably to computers, i would >> > suggest >> > you to install the pre-compiled binaries. then all you need to do is >> > just >> > define an environmental variable or just source the path every time you >> > run >> > it. You can check the software by running a small minimization using the >> > minimize module of timer (it will be in the $tinkerhome/bin/minimize or >> > $tinkerhome/minimize path). But you need to create an xyz file with all >> > connectivities properly before you can use it. >> > >> > >> > i hope it helps you. >> > regards, >> > ArunKumar. S. >> > >> > >> > >> > On Fri, May 13, 2011 at 11:15 AM, Amrita Kumari amrita.g13#%#gmail.com >> > wrote: >> >> >> >> Sent to CCL by: "Amrita  Kumari" [amrita.g13[]gmail.com] >> >> Dear all, >> >> >> >> I am a new user of TINKER software. I have downloaded and installed it >> >> on my 32bit Linux system. But I don't know how to check whether it has >> >> been installed properly or not. I used command: ./compile.make, >> >> ./library.make and ./link.make for installation and it has produced >> >> the complete set of TINKER executables. But I don't know how to test >> >> this software means how to give input and get output. >> >> >> >> Thanks, >> >> Amrita Kumari >> >> Research Scholar >> >> IISER Mohali >> >> Chandigarh (INDIA).>> >> To recover the email address of the author of the message, please >> >> change>> >>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>> >>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>> >>      http://www.ccl.net/chemistry/sub_unsub.shtml>> >>      http://www.ccl.net/spammers.txt>> >> >> >> >> > >> > > > From owner-chemistry@ccl.net Tue May 17 06:32:01 2011 From: "masume - gharabaghi gharabaghimasume66*_*gmail.com" To: CCL Subject: CCL:G: pcm o9 Message-Id: <-44669-110517044933-18056-Dh6jtSH7jJ41ge0pV7ARCw/./server.ccl.net> X-Original-From: "masume - gharabaghi" Date: Tue, 17 May 2011 04:49:30 -0400 Sent to CCL by: "masume - gharabaghi" [gharabaghimasume66###gmail.com] Hi alls; its long time i'm concerning with pcm calculation via G09 package.in the case of calculating of pcm energy i have problem with bellow terms which emerg clearly in G03 out put: Total non electrostatic Polarized solute)-Solvent Total free energy in solution would you mind helping me how to find this terms in G09 out put. in advance, thanks for your attention. From owner-chemistry@ccl.net Tue May 17 07:07:01 2011 From: "Xiaohui Kang huixiaokang328#%#163.com" To: CCL Subject: CCL:G: some problems on Gaussian09 Message-Id: <-44670-110517064403-6444-HqWgSsZoNjeUKwXZ60ix6Q[a]server.ccl.net> X-Original-From: "Xiaohui Kang" Date: Tue, 17 May 2011 06:44:00 -0400 Sent to CCL by: "Xiaohui Kang" [huixiaokang328#163.com] Dear cclers: I come across some problems which influence my research. I hope you can give me some helps,and help me solve my questions.I use the gaussian09 program. first: "H-V products w/o non-bonded: 30 SchOr2 failed for MMProj. Error termination via Lnk1e in /home/xkang/bin/g09/l103.exe at Sun Apr 10 11:19:32 2011. Job cpu time: 0 days 20 hours 59 minutes 23.9 seconds. File lengths (MBytes): RWF= 122 Int= 0 D2E= 0 Chk= 18 Scr= 1" what's reason leading to this err in my oniom calculations, are there some methods to resolve this problem? Seond: OrtVc1 failed #1. Error termination via Lnk1e in /work1/soft/g09/l103.exe at Sat Mar 12 01:31:15 2011. Job cpu time: 0 days 16 hours 26 minutes 16.1 seconds. File lengths (MBytes): RWF= 1320 Int= 0 D2E= 0 Chk= 24 Scr= 1 (END) third: Could "opt" and "stable=opt" be used at the same time? Any help would be appreciated,thank you very much! Sincerely yous! xkang From owner-chemistry@ccl.net Tue May 17 07:42:01 2011 From: "Xiaohui Kang huixiaokang328-,-163.com" To: CCL Subject: CCL:G: some problems on Gaussian09 Message-Id: <-44671-110517064426-6915-6wKlPeCehOBljORFADvong===server.ccl.net> X-Original-From: "Xiaohui Kang" Date: Tue, 17 May 2011 06:44:25 -0400 Sent to CCL by: "Xiaohui Kang" [huixiaokang328#163.com] Dear cclers: I come across some problems which influence my research. I hope you can give me some helps,and help me solve my questions.I use the gaussian09 program. first: "H-V products w/o non-bonded: 30 SchOr2 failed for MMProj. Error termination via Lnk1e in /home/xkang/bin/g09/l103.exe at Sun Apr 10 11:19:32 2011. Job cpu time: 0 days 20 hours 59 minutes 23.9 seconds. File lengths (MBytes): RWF= 122 Int= 0 D2E= 0 Chk= 18 Scr= 1" what's reason leading to this err in my oniom calculations, are there some methods to resolve this problem? Seond: OrtVc1 failed #1. Error termination via Lnk1e in /work1/soft/g09/l103.exe at Sat Mar 12 01:31:15 2011. Job cpu time: 0 days 16 hours 26 minutes 16.1 seconds. File lengths (MBytes): RWF= 1320 Int= 0 D2E= 0 Chk= 24 Scr= 1 (END) third: Could "opt" and "stable=opt" be used at the same time? Any help would be appreciated,thank you very much! Sincerely yous! xkang From owner-chemistry@ccl.net Tue May 17 08:16:00 2011 From: "Ramachandran Chelat rcchelat+*+gmail.com" To: CCL Subject: CCL:G: PBC calculations using gaussian Message-Id: <-44672-110517074007-15902-7eLbUZAueechymmo1cTGpA=-=server.ccl.net> X-Original-From: "Ramachandran Chelat" Date: Tue, 17 May 2011 07:40:04 -0400 Sent to CCL by: "Ramachandran Chelat" [rcchelat/./gmail.com] Dear CCL users, Can anyone suggest me some papers on PBC calculations using GAUSSIAN program Thanks in advance Rama From owner-chemistry@ccl.net Tue May 17 08:51:00 2011 From: "Ramachandran Chelat rcchelat[*]rediffmail.com" To: CCL Subject: CCL:G: PBC calculations using gaussian Message-Id: <-44673-110517071454-15994-wfqkPnprcf1AmWVsjtCkkA++server.ccl.net> X-Original-From: "Ramachandran Chelat" Date: Tue, 17 May 2011 07:14:51 -0400 Sent to CCL by: "Ramachandran Chelat" [rcchelat^-^rediffmail.com] Dear Friends, Please suggest some papers on PBC calculations using GAUSSIAN program Thanks in advance Rama From owner-chemistry@ccl.net Tue May 17 09:29:01 2011 From: "Mehboob Alam mehboob.cu^-^gmail.com" To: CCL Subject: CCL:G: some problems on Gaussian09 Message-Id: <-44674-110517092742-9918-rJgIw2zR/3KJ03w7m2ylcQ^^^server.ccl.net> X-Original-From: Mehboob Alam Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 17 May 2011 18:57:31 +0530 MIME-Version: 1.0 Sent to CCL by: Mehboob Alam [mehboob.cu[*]gmail.com] Hello Xkang, As far as I know the l103.exe error is due to the the problem with constrained coordinates. One of the solution to this problem is to restart the calculation with some other input geometry. Hope it will be useful. Best of luck. Mehboob On 5/17/11, Xiaohui Kang huixiaokang328-,-163.com wrote: > > Sent to CCL by: "Xiaohui Kang" [huixiaokang328#163.com] > Dear cclers: > I come across some problems which influence my research. I hope you can > give me some helps,and help me solve my questions.I use the gaussian09 > program. > first: > > "H-V products w/o non-bonded: 30 > SchOr2 failed for MMProj. > Error termination via Lnk1e in /home/xkang/bin/g09/l103.exe at Sun Apr 10 > 11:19:32 2011. > Job cpu time: 0 days 20 hours 59 minutes 23.9 seconds. > File lengths (MBytes): RWF= 122 Int= 0 D2E= 0 Chk= 18 > Scr= 1" > > what's reason leading to this err in my oniom calculations, are there some > methods to resolve this problem? > Seond: > > OrtVc1 failed #1. > Error termination via Lnk1e in /work1/soft/g09/l103.exe at Sat Mar 12 > 01:31:15 2011. > Job cpu time: 0 days 16 hours 26 minutes 16.1 seconds. > File lengths (MBytes): RWF= 1320 Int= 0 D2E= 0 Chk= 24 > Scr= 1 > (END) > > third: > > Could "opt" and "stable=opt" be used at the same time? > > Any help would be appreciated,thank you very much! > > > Sincerely yous! > > xkang> > > From owner-chemistry@ccl.net Tue May 17 10:42:00 2011 From: "Mehboob Alam mehboob.cu.]=[.gmail.com" To: CCL Subject: CCL:G: PBC calculations using gaussian Message-Id: <-44675-110517104033-7699-995VNH2IwKtpkFCtZ9G9Zw]=[server.ccl.net> X-Original-From: Mehboob Alam Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 17 May 2011 20:10:21 +0530 MIME-Version: 1.0 Sent to CCL by: Mehboob Alam [mehboob.cu++gmail.com] Hello Ram, Although I've never done PBC calculation but while internet surfing I found a pdf file relating to this. The link is http://scuseria.rice.edu/gau/gdv_pbc/pbc_guide.pdf Hope it will help. Best of luck Mehboob On 5/17/11, Ramachandran Chelat rcchelat[*]rediffmail.com wrote: > > Sent to CCL by: "Ramachandran Chelat" [rcchelat^-^rediffmail.com] > Dear Friends, > Please suggest some papers on PBC calculations using GAUSSIAN program > > Thanks in advance > Rama> > > From owner-chemistry@ccl.net Tue May 17 11:17:00 2011 From: "John McKelvey jmmckel{:}gmail.com" To: CCL Subject: CCL:G: Use of Ram Disk Message-Id: <-44676-110517102545-30727-38JxFbzyuVIRSM2F80GYCQ.:.server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=0003255593be992dd604a3798b75 Date: Tue, 17 May 2011 10:25:35 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel]![gmail.com] --0003255593be992dd604a3798b75 Content-Type: text/plain; charset=ISO-8859-1 Folks, Has anyone successfully used linux ram-disk, /dev/shm, for Gaussian RW files? John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel\a/gmail.com --0003255593be992dd604a3798b75 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Folks,

Has anyone successfully used linux ram-disk, /dev/shm, for Ga= ussian RW files?

John

--
John McKelvey
1= 0819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel\a/gmail.com
--0003255593be992dd604a3798b75-- From owner-chemistry@ccl.net Tue May 17 11:52:00 2011 From: "Pierre Archirel pierre.archirel#u-psud.fr" To: CCL Subject: CCL:G: basis sets Message-Id: <-44677-110517102841-968-cQh0tjDwxnUX350HDx7A/w(-)server.ccl.net> X-Original-From: "Pierre Archirel" Date: Tue, 17 May 2011 10:28:38 -0400 Sent to CCL by: "Pierre Archirel" [pierre.archirel**u-psud.fr] This is a comment on a recent question about basis sets: 1- one colleague is looking for the best basis set for a CNOH molecule 2- several colleagues state that 6-31g(d) works rather well and is largely used 3- I state that SDD (Stuttgart-Dresden) bases are smaller and more accurate than any Pople basis, and that I have published a comparison of the bases in the conformation analysis of a CNOH molecule (Tetrahedron 64 (2008) 1743) I acknowledge that this comparison is for one molecule only, not a list. 4- the first colleagues thanks for advices and will choose 6-31g(d) bases. My question is: why don't you use SDD bases? are you afraid of core pseudos? (of course they cannot be used in NMR calculations) or of giving explicitely polarisation gaussians? Or do you use them because it is very likely that your referees use them also? If you simply prefer Pople bases because many people use them, I emphasize that 6-31+g(d) is the best (small) Pople basis, much better than 6-31g(d). Nevertheless, SDD is still better, and smaller. Pierre Archirel LCP Universite Paris-Sud Orsay, France From owner-chemistry@ccl.net Tue May 17 13:13:00 2011 From: "=?ISO-8859-1?Q?Jo=E3o_Henriques?= joao.henriques.32353===gmail.com" To: CCL Subject: CCL: which basis set Message-Id: <-44678-110517130442-28807-MSquwZAphOneGZ3KEO+lqA++server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Jo=E3o_Henriques?= Content-Type: multipart/alternative; boundary=bcaec520eea3f3592704a37bc398 Date: Tue, 17 May 2011 10:04:30 -0700 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Jo=E3o_Henriques?= [joao.henriques.32353[-]gmail.com] --bcaec520eea3f3592704a37bc398 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Arslan, You are most welcome. This basis set should take care of most charged species consituted by CHNO. However, anions may benefit from the inclusion of diffuse functions. Any good textbook should give you further insight on this subject. Once again, remember that we're speaking of CHNO systems. Transition elements require special basis sets and are a lot more troublesome. Geometr= y optimization of paramagnetic systems can easily become a nightmare... Best regards, On Mon, May 16, 2011 at 8:43 AM, arslan ali arslanali1986*gmail.com < owner-chemistry-*-ccl.net> wrote: > > Sent to CCL by: arslan ali [arslanali1986=3Dgmail.com] > hello dear Jo=E3o Henriques, > > i am very thankfull for your valuable reply, are these basis sets > "6-31G(d) (Valence Double Zeta + Polarization (Li-Ar)" also good for > charged species? > > > regards > Arslan > > On 5/12/11, Jo=E3o Henriques joao.henriques.32353*gmail.com > wrote: > > Hi Arslan, > > > > Well it depends on your final objective and how accurate you want the > > computation to be. This subject is non-black-box. However I would > recommend > > 6-31G(d) (Valence Double Zeta + Polarization (Li-Ar)). It is relatively > > accurate and not that computationally expensive. Most publications in t= he > > field use this basis set for this type of calculation on CHNO elements. > > > > Regards, > > > > On Tue, May 10, 2011 at 7:06 AM, arslan ali arslanali1986{:}gmail.com < > > owner-chemistry() ccl.net> wrote: > > > >> hi, > >> > >> can anybody please tell me, which basis set in DFT will be more > >> appropriate > >> for geometry optimization of molecules of aprox 500 amu containing CHN= O > >> elements only?? > >> > >> thanks in advance > >> > >> Arslan > >> > > > > > > > > -- > > Jo=E3o Henriques, MSc in Biochemistry > > Faculty of Science of the University of Lisbon > > Department of Chemistry and Biochemistry > > C8 Building, Room 8.5.47 > > Campo Grande, 1749-016 Lisbon, Portugal > > E-mail: joao.henriques.32353() gmail.com / jmhenriques() fc.ul.pt > > http://intheochem.fc.ul.pt/members/joaoh.html > > > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Jo=E3o Henriques, MSc in Biochemistry Faculty of Science of the University of Lisbon Department of Chemistry and Biochemistry C8 Building, Room 8.5.47 Campo Grande, 1749-016 Lisbon, Portugal E-mail: joao.henriques.32353-*-gmail.com / jmhenriques-*-fc.ul.pt http://intheochem.fc.ul.pt/members/joaoh.html --bcaec520eea3f3592704a37bc398 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Arslan,
=A0
You are most welcome.=A0This basis set=A0should take care of most char= ged species=A0consituted by CHNO.=A0However, anions=A0may=A0benefit from th= e inclusion of diffuse functions. Any good textbook should give you further= insight on this subject.
=A0
Once again, remember that we're speaking of CHNO systems. Transiti= on elements require special basis sets and are a lot more troublesome. Geom= etry optimization of paramagnetic systems=A0can easily become a nightmare..= .
=A0
Best regards,
On Mon, May 16, 2011 at 8:43 AM, arslan ali arsl= anali1986*gmail.com <= owner-chemistry-*-ccl.net><= /span> wrote:

Sent to CCL by: arslan ali [= arslanali1986=3Dgmail.com]
hello dear Jo=E3o Henriques,

i am very thankfull for your valuable r= eply, are these basis sets
"6-31G(d) (Valence Double Zeta + Polariz= ation (Li-Ar)" also good for
charged species?


regards Arslan

On 5/12/11, Jo=E3o Henriques joao.henriques.32353*gmail.com
<owner-chemistry(_= )ccl.net> wrote:
&g= t; Hi Arslan,
>
> Well it depends on your final objective and how accurate you w= ant the
> computation to be. This subject is non-black-box. However I= would recommend
> 6-31G(d) (Valence Double Zeta + Polarization (Li-A= r)). It is relatively
> accurate and not that computationally expensive. Most publications in = the
> field use this basis set for this type of calculation on CHNO e= lements.
>
> Regards,
>
> On Tue, May 10, 2011 at 7= :06 AM, arslan ali arslanali1986{:}gmail.com <
> owner-chemistry() ccl.ne= t> wrote:
>
>> hi,
>>
>> can anybod= y please tell me, which basis set in DFT will be more
>> appropria= te
>> for geometry optimization of molecules of aprox 500 amu containing= CHNO
>> elements only??
>>
>> thanks in advance=
>>
>> Arslan
>>
>
>
>
> --
> Jo=E3o Henriques, MSc in Biochemistry
> Faculty of Sc= ience of the University of Lisbon
> Department of Chemistry and Bioch= emistry
> C8 Building, Room 8.5.47
> Campo Grande, 1749-016 Lis= bon, Portugal
> E-mail: joao.henriques.32353() gmail.com / jmhenriques() fc.ul.pt
> http://intheochem.fc.ul.pt/members/joaoh.= html
>



-=3D This is automatically added to each message by the= mailing script =3D-
To recover the email address of the author of the m= essage, please change
the strange characters on the top line to the -*- si= gn. You can also
E-mail to subs= cribers: CHEMISTRY-*-ccl.net or use:=
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: = CHEMISTRY-REQUEST-*-ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cg= i-bin/ccl/send_ccl_message

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

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

Job: http://www.c= cl.net/jobs
Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.sht= ml
=A0= =A0 =A0http:= //www.ccl.net/spammers.txt

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




--
Jo=E3o Henriqu= es, MSc in Biochemistry
Faculty of Science of the University of Lisbon
Department of Chemistry a= nd Biochemistry
C8 Building, Room 8.5.47
Campo Grande, 1749-016 Lisbo= n, Portugal
E-mail: joao.henriques.32353-*-gmail.com /=A0jmhenriques-*-fc.ul.pt=20
--bcaec520eea3f3592704a37bc398-- From owner-chemistry@ccl.net Tue May 17 13:48:00 2011 From: "kimshu kamao kimshukanmo^gmail.com" To: CCL Subject: CCL: gradient Message-Id: <-44679-110517131331-16682-fYCuBQgr8t0aQrQonCNlTg[#]server.ccl.net> X-Original-From: "kimshu kamao" Date: Tue, 17 May 2011 13:13:29 -0400 Sent to CCL by: "kimshu kamao" [kimshukanmo%a%gmail.com] Hi Group, i would be grateful if someone can let me know as to how to know whether the gradient is changing or not in softwares like molpro or any other one. suppose i optimize one structure with molpro and I check whether it is really the optimized one with another software (advanced version), then how do i confirm about it. if the answer is that gradient should be zero in both, then how to see them in output files. thanks a lot. kim From owner-chemistry@ccl.net Tue May 17 14:23:00 2011 From: "=?ISO-8859-1?Q?Jo=E3o_Henriques?= joao.henriques.32353-*-gmail.com" To: CCL Subject: CCL:G: basis sets Message-Id: <-44680-110517131242-16390-h+TnD3WRrbpdh+WzOxFlOA{=}server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Jo=E3o_Henriques?= Content-Type: multipart/alternative; boundary=bcaec520e99ba26e4d04a37be0a0 Date: Tue, 17 May 2011 10:12:31 -0700 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Jo=E3o_Henriques?= [joao.henriques.32353|*|gmail.com] --bcaec520e99ba26e4d04a37be0a0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Pierre, What can I say? You may have published a comparison of the bases and found that SDD are better suited for this type of job, but 6-31G(d) still remains more popular. People will eventually start using SDD if more studies suppor= t your findings. Going 'Charlie Sheen' on this subject is not likely to help your cause. Paradigms take some time to change. Just be patient. By the way, I have nothing against core pseudos. I actually used them in my previous work and they worked a lot better than any other 'complete' basis set I tried. Best regards, On Tue, May 17, 2011 at 7:28 AM, Pierre Archirel pierre.archirel#u-psud.fr = < owner-chemistry%a%ccl.net> wrote: > > Sent to CCL by: "Pierre Archirel" [pierre.archirel**u-psud.fr] > This is a comment on a recent question about basis sets: > 1- one colleague is looking for the best basis set for a CNOH molecule > 2- several colleagues state that 6-31g(d) works rather well and is largel= y > used > 3- I state that SDD (Stuttgart-Dresden) bases are smaller and more accura= te > than any Pople basis, and that I have published a comparison of the bases= in > the conformation analysis of a CNOH molecule (Tetrahedron 64 (2008) 1743) > I acknowledge that this comparison is for one molecule only, not a list. > 4- the first colleagues thanks for advices and will choose 6-31g(d) bases= . > > My question is: why don't you use SDD bases? are you afraid of core > pseudos? > (of course they cannot be used in NMR calculations) or of giving > explicitely polarisation gaussians? Or do you use them because it is very > likely that your referees use them also? > > If you simply prefer Pople bases because many people use them, I emphasiz= e > that 6-31+g(d) is the best (small) Pople basis, much better than 6-31g(d)= . > Nevertheless, SDD is still better, and smaller. > > Pierre Archirel > LCP > Universite Paris-Sud > Orsay, France > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Jo=E3o Henriques, MSc in Biochemistry Faculty of Science of the University of Lisbon Department of Chemistry and Biochemistry C8 Building, Room 8.5.47 Campo Grande, 1749-016 Lisbon, Portugal E-mail: joao.henriques.32353%a%gmail.com / jmhenriques%a%fc.ul.pt http://intheochem.fc.ul.pt/members/joaoh.html --bcaec520e99ba26e4d04a37be0a0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Pierre,
=A0
What can I say? You may have published a comparison of the bases and f= ound that SDD are better suited for this type of job, but 6-31G(d) still re= mains more popular. People will eventually start using SDD if more studies = support your findings. Going 'Charlie Sheen' on this subject is not= likely to help your cause. Paradigms take some time to change. Just be pat= ient.
=A0
By the way, I have nothing against core pseudos. I actually used them = in my previous work and they worked a lot better than any other 'comple= te' basis set I tried.
=A0
Best regards,
On Tue, May 17, 2011 at 7:28 AM, Pierre Archirel= pierre.archirel#u-psud.fr <owner-chemistry%a%ccl.net> wrote:

Sent to CCL by: "Pierre= =A0Archirel" [pierre.archirel**u-psud.fr]
This is a comment on a recent question about basis sets:
1- one colleagu= e is looking for the best basis set for a CNOH molecule
2- several colle= agues state that 6-31g(d) works rather well and is largely used
3- I sta= te that SDD (Stuttgart-Dresden) bases are smaller and more accurate than an= y Pople basis, and that I have published a comparison of the bases in the c= onformation analysis of a CNOH molecule (Tetrahedron 64 (2008) 1743)
I acknowledge that this comparison is for one molecule only, not a list.4- the first colleagues thanks for advices and will choose 6-31g(d) bases.=

My question is: why don't you use SDD bases? are you afraid of = core pseudos?
(of course they cannot be used in NMR calculations) or of giving explicitel= y polarisation gaussians? Or do you use them because it is very likely that= your referees use them also?

If you simply prefer Pople bases becau= se many people use them, I emphasize that 6-31+g(d) is the best (small) Pop= le basis, much better than 6-31g(d). Nevertheless, SDD is still better, and= smaller.

Pierre Archirel
LCP
Universite Paris-Sud
Orsay, France

=

-=3D This is automatically added to each message by the mailing scr= ipt =3D-
To recover the email address of the author of the message, plea= se changelook = up the X-Original-From: line in the mail header.

E-mail to subscribe= rs: CHEMISTRY%a%ccl.net or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-= mail to administrators: CHEMIS= TRY-REQUEST%a%ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Su= bscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.s= html

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

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/<= br>
Search Messages: http://www.ccl.net/chemistry/searchccl/index.sht= ml
=A0= =A0 =A0http:= //www.ccl.net/spammers.txt

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




--
Jo=E3o Henriqu= es, MSc in Biochemistry
Faculty of Science of the University of Lisbon
Department of Chemistry a= nd Biochemistry
C8 Building, Room 8.5.47
Campo Grande, 1749-016 Lisbo= n, Portugal
E-mail: joao.henriques.32353%a%gmail.com /=A0jmhenriques%a%fc.ul.pt=20
--bcaec520e99ba26e4d04a37be0a0-- From owner-chemistry@ccl.net Tue May 17 14:58:01 2011 From: "Gerald Knizia knizia * theochem.uni-stuttgart.de" To: CCL Subject: CCL:G: basis sets Message-Id: <-44681-110517140909-4818-BSd8U1Mt5/y4jspX7c3bew(~)server.ccl.net> X-Original-From: Gerald Knizia Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 17 May 2011 14:08:59 -0400 MIME-Version: 1.0 Sent to CCL by: Gerald Knizia [knizia{}theochem.uni-stuttgart.de] Pierre Archirel pierre.archirel#u-psud.fr wrote: > Sent to CCL by: "Pierre Archirel" [pierre.archirel**u-psud.fr] > This is a comment on a recent question about basis sets: > 1- one colleague is looking for the best basis set for a CNOH molecule > 2- several colleagues state that 6-31g(d) works rather well and is largely used > 3- I state that SDD (Stuttgart-Dresden) bases are smaller and more accurate than any Pople basis, and that I have published a comparison of the bases in the conformation analysis of a CNOH molecule (Tetrahedron 64 (2008) 1743) > I acknowledge that this comparison is for one molecule only, not a list. > 4- the first colleagues thanks for advices and will choose 6-31g(d) bases. > Well, first: Basis set issues are complicated, and data on only one molecule does not say very much at all. When developing basis sets, you will often find that a set works well for 19 diverse molecules and then gives large errors for the 20th. This is not to say that the SSD sets are bad; the people who made them know what they are doing. Just a general comment on the comparison you cite. Apart from that, there are other basis sets which are known to be superior to the Pople sets. E.g., Weigends def2 sets (the Turbomole sets) are superior on all accounts, especially for SCF calculations. And they even come with auxiliary fitting sets for all elements. The cc-pVnZ families are certainly better for correlated calculations than Pople sets and allow for approaching basis set limits systematically and closely. While I can understand why the cc-sets are not often used in Gaussian calculations (they are not optimal for SCF, and a program which can't deal well with general contractions certainly doesn't like cc-sets), I do wonder why people don't simply stop using Pople sets and use def2 sets instead. I hope the main reason is that for DFT calculations the basis sets really don't matter that much, and you're more or less fine with the Pople sets, too. Of course this kind of defeats the point of asking about basis sets in the first place. -- Gerald Knizia From owner-chemistry@ccl.net Tue May 17 17:40:01 2011 From: "Giuseppe Mallia g.mallia,,imperial.ac.uk" To: CCL Subject: CCL: MSSC2011 - Ab initio Modelling in Solid State Chemistry Message-Id: <-44682-110517172223-7861-B4jnB1a3r92AZNFFflyiRw^^server.ccl.net> X-Original-From: "Giuseppe Mallia" Date: Tue, 17 May 2011 17:22:20 -0400 Sent to CCL by: "Giuseppe Mallia" [g.mallia%imperial.ac.uk] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ WORKSHOP ANNOUNCEMENTS MSSC2011 - Ab initio Modelling in Solid State Chemistry ==> Turin Edition (Experienced Users): Featuring CRYSTAL09 and CRYSCOR ==> London Edition (New Users): Discovering quantum-mechanical simulations with CRYSTAL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MSSC2011 - Ab initio Modelling in Solid State Chemistry Turin Edition (Experienced Users): Featuring CRYSTAL09 and CRYSCOR http://www.crystal.unito.it/mssc2011 Torino, Italy, September 4-9, 2011 Directors: R. Dovesi - C. Pisani Its aim is to illustrate the features of the CRYSTAL09 and CRYSCOR09 programs: CRYSTAL09 main new features include: transition state search, phonon dispersion, linear and non-linear dielectric properties through the CPHF/CPKS scheme, automated calculation of EOS and elastic constants, exploitation of special symmetry for nanotubes and helices, and more. CRYSCOR09 is the first publicly distribute code that allows to compute the MP2 correlation energy of periodic structures. The school is addressed to all CRYSTAL's users, senior researchers and scientists with a good background in solid state chemistry and physics, who can take advantage of the two codes for their applications Memorial Carla Roetti On September 7th, there will be a day in memory of Carla Roetti. Eminent scientists (E. Clementi, F. Illas, ...) will give a survey on the development of theoretical and computational chemistry from molecules to solids and viceversa. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MSSC2011 - Ab initio Modelling in Solid State Chemistry London Edition (New Users): Discovering quantum-mechanical simulations with CRYSTAL http://www.cse.scitech.ac.uk/events/MSSC2011/ London (UK), September 19-23, 2011 Directors: N.M. Harrison - G. Mallia The week long school is designed for CRYSTAL users, PhD students, Post-Docs and researchers with interests in solid state chemistry, physics, materials science, surface science, catalysis, magnetism and nano-science. It will provide both an introduction to the capabilities of quantum mechanical simulation and to the practical use of CRYSTAL09 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-chemistry@ccl.net Tue May 17 18:16:01 2011 From: "Stephan Ehrlich stephan.ehrlich _ uni-muenster.de" To: CCL Subject: CCL: dft-d3 for large systems Message-Id: <-44683-110517105101-14712-P2GK8/LVa9GcEdWp4ISlew%server.ccl.net> X-Original-From: "Stephan Ehrlich" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes Date: Tue, 17 May 2011 16:50:49 +0200 MIME-Version: 1.0 Sent to CCL by: "Stephan Ehrlich" [stephan.ehrlich(~)uni-muenster.de] Dear CCL subscribers, we have uploaded a new version of our free dftd3 code, a general dispersion correction for density functional theory (and other methods). The main improvement is the introduction of reasonable cutoffs for the gradient (which formerly scaled N^3). This makes it possible to use the code also with semi-empirical and FF methods and large (>1000 atoms) systems. The manual was also updated. The code is freely available on our group homepage: http://www.uni-muenster.de/Chemie.oc/grimme/ Cheers, Stephan Ehrlich. -- Stephan Ehrlich Organisch-Chemisches Institut (Abt. Theoretische Chemie) Westfaelische Wilhelms-Universitaet Corrensstrasse 40 D-48149 Muenster Tel: +49-(0)251-83 33289 Email: stephan.ehrlich(~)uni-muenster.de From owner-chemistry@ccl.net Tue May 17 21:33:00 2011 From: "Andrew Orry andy-*-molsoft.com" To: CCL Subject: CCL: iPhone & iPad 3D Molecule Browser - iMolview Message-Id: <-44684-110517213210-26509-h3+8LACW4f12LiGw3m5arA^-^server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Tue, 17 May 2011 18:28:38 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy]![molsoft.com] On 5/7/2011 2:43 AM, Arne Dieckmann adieckma-$-googlemail.com wrote: > Sent to CCL by: Arne Dieckmann [adieckma],[googlemail.com] > Dear Andrew, > > how about loading in your own pdb files? I'd buy it if that will be possible. > The latest version of iMolview (v1.2) is now synced with iTunes so you can load in your own PDB files from there. We also fixed a graphics issue with older iPhone/iPod devices and introduced a number of other features and improvements. Please see the app page for the full release notes:http://www.molsoft.com/iMolview.html Thanks, Andrew -- Andrew Orry Ph.D. MolSoft LLC Senior Research Scientist 11199 Sorrento Valley Road, S209 San Diego CA 92121 Tel: 858-625-2000 x108 Fax: 828-625-2888 www.molsoft.com From owner-chemistry@ccl.net Tue May 17 22:08:00 2011 From: "Gilles MARCOU g.marcou.:.unistra.fr" To: CCL Subject: CCL: Chemoinformatics Message-Id: <-44685-110517144525-18712-U56pJdQr49jtuKLkAxerzQ%x%server.ccl.net> X-Original-From: "Gilles MARCOU" Date: Tue, 17 May 2011 14:45:22 -0400 Sent to CCL by: "Gilles MARCOU" [g.marcou*o*unistra.fr] Dear all, Chemoinformatics is young discipline with a curiculum organized around molecular descriptors, chemical space and data mining. It is different from Molecular Modeling and Quantum Chemistry although it boroughs from these disciplines. It is different also from Bioinformatics although it has proven its usefullness mostly in the area of drug design. The University of Strasbourg in France, is organizing since 2000, a master level diploma in chemoinformatics. You can find a complete description of this master on its web site (http://infochimie.u-strasbg.fr/master/master_home.htm). Beside, we organize also a 5 days short courses "Introduction to chemoinformatics (http://infochim.u-strasbg.fr/spip.php?rubrique123). This could also be seen as a an example of Chemoinformatics curriculum. Furthermore, we organize every two year a summer school in chemoinformatics, the last session being in 2010 (http://infochim.u-strasbg.fr/spip.php?rubrique12) and the next session will be in June 2012. Finaly, there exists a French Society of Chemoinformatics (http://www.chemoinformatique.fr/) which is close to the Internation Chemoinformatics and QSAR Society (http://www.chemoinformatique.fr/modules/weblinks/visit.php?lid=5). I hope those links will be helpful to clarify the picture of Chemoinformatics today. Yours Faithfully, Gilles Marcou