From owner-chemistry@ccl.net Sat May 10 00:26:00 2014 From: "Ravidas ambekemo[A]gmail.com" To: CCL Subject: CCL: Sites you need to visit - CEO, Ravidas Message-Id: <-50070-140509215034-4455-3kM/pz5UP4wgxvIMYxTJwA .. server.ccl.net> X-Original-From: "Ravidas" Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; charset="UTF-8"; boundary="b1_0cd174dc5cf10101687abdfc1d57297f" Date: Fri, 09 May 2014 17:40:17 -0500 MIME-Version: 1.0 Sent to CCL by: "Ravidas" [ambekemo_-_gmail.com] --b1_0cd174dc5cf10101687abdfc1d57297f Content-Type: text/plain; format=flowed; charset="UTF-8" Content-Transfer-Encoding: 8bit Your email client cannot read this email. To view it online, please go here: http://ravin-das.com/web/display.php?M=3935923&C=92352b72088f68add8b1126736ea7a00&S=171&L=113&N=45 To stop receiving these emails:http://ravin-das.com/web/unsubscribe.php?M=3935923&C=92352b72088f68add8b1126736ea7a00&L=113&N=171 --b1_0cd174dc5cf10101687abdfc1d57297f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: 8bit

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--b1_0cd174dc5cf10101687abdfc1d57297f-- From owner-chemistry@ccl.net Sat May 10 06:42:00 2014 From: "edulsa:+:ufpr.br" To: CCL Subject: CCL: Trying to find Sirius Visualization Software Message-Id: <-50071-140510064015-13366-APXAUPT2ISiNCRvfz8GO2A!A!server.ccl.net> X-Original-From: edulsa.:.ufpr.br Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Sat, 10 May 2014 07:40:07 -0300 MIME-Version: 1.0 Sent to CCL by: edulsa{:}ufpr.br Sirs and Ladies I am trying to find a Sirius (software to visualize molecules and proteins). I found links to this at San Diego Supercomputer Center (sirius.sdsc.edu) and http://www.ngbw.org/sirius/downloads.php, however all of them are broken. Of course, Google points to me a lot of software called Sirius that are able to perform a lot of tasks, but none related to computational chemistry in essence. Please, could you help me? Thank you in advance Yours Eduardo Eduardo Lemos de Sa Associated Professor at Chemistry Department Universidade Federal do Parana Dep. Quimica, P. Box 19081, 81531-990 Curitiba PR / Brazil phone: +55(41)33613300 fax : +55(41)33613186 Voip Number: call to (41) 33613600 (listen to the message and type 10531185) From owner-chemistry@ccl.net Sat May 10 12:15:00 2014 From: "Flick Coleman wcoleman..wellesley.edu" To: CCL Subject: CCL: Trying to find Sirius Visualization Software Message-Id: <-50072-140510102534-20100-MCMfOy9MFnnxximHOf+l7w++server.ccl.net> X-Original-From: Flick Coleman Content-Type: multipart/alternative; boundary=089e01493df646d32904f90c7ce0 Date: Sat, 10 May 2014 10:24:46 -0400 MIME-Version: 1.0 Sent to CCL by: Flick Coleman [wcoleman/./wellesley.edu] --089e01493df646d32904f90c7ce0 Content-Type: text/plain; charset=UTF-8 A google search for "sirius molecular visualization" gives many results for the software. Try sirius3.software.informer.com/1.2/ Cheers, Flick _______________ William F. Coleman Professor Emeritus of Chemistry Wellesley College Wellesley MA 02481 On Sat, May 10, 2014 at 6:40 AM, edulsa:+:ufpr.br wrote: > > Sent to CCL by: edulsa{:}ufpr.br > Sirs and Ladies > > I am trying to find a Sirius (software to visualize molecules and > proteins). I found links to this at San Diego Supercomputer Center ( > sirius.sdsc.edu) and http://www.ngbw.org/sirius/downloads.php, however > all of them are broken. Of course, Google points to me a lot of software > called Sirius that are able to perform a lot of tasks, but none related to > computational chemistry in essence. Please, could you help me? > > Thank you in advance > > Yours > > > Eduardo > > > Eduardo Lemos de Sa > Associated Professor at Chemistry Department > Universidade Federal do Parana > Dep. Quimica, P. Box 19081, 81531-990 Curitiba PR / Brazil > phone: +55(41)33613300 > fax : +55(41)33613186 > Voip Number: call to (41) 33613600 (listen to the message and > type 10531185)http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: http://server.ccl.net/ > chemistry/announcements/conferences/> > > --089e01493df646d32904f90c7ce0 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
A google search for "sirius molecular= visualization" gives many results for the software. Try sirius3.software.informer.com/1.2/=



Cheers,

Flick

_______________

William= F. Coleman
Professor Emeritus of Chemistry
Wellesl= ey College
Wellesley MA 02481




On Sat, May 10, 2014 at 6:40 AM, edulsa:= +:ufpr.br <owner-chemistry\a/ccl.net> wrote:

Sent to CCL by: edulsa{:}
ufpr.= br
Sirs and Ladies

I am trying to find a Sirius (software to visualize molecules and proteins)= . I found links to this at San Diego Supercomputer Center (sirius.sdsc.edu) and http://www.ngbw.o= rg/sirius/downloads.php, however all of them are broken. Of cour= se, Google points to me a lot of software called Sirius that are able to pe= rform a lot of tasks, but none related to computational chemistry in essenc= e. Please, could you help me?

Thank you in advance

Yours


Eduardo


Eduardo Lemos de Sa
Associated Professor at Chemistry Department
Universidade Federal do Parana
Dep. Quimica, P. Box 19081, 81531-990 Curitiba PR / Brazil
phone: +55(41)33613300
fax =C2=A0: +55(41)33613186
Voip Number: call to (41) 33613600 (listen to the message and
type 10531185)



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--089e01493df646d32904f90c7ce0-- From owner-chemistry@ccl.net Sat May 10 14:27:01 2014 From: "Ronald Cook cookrl*o*tda.com" To: CCL Subject: CCL:G: Gaussian processor Message-Id: <-50073-140509223512-22719-nZPh83krMJWY1PEv6XWyNQ- -server.ccl.net> X-Original-From: Ronald Cook Content-Type: multipart/alternative; boundary=20cf301af5d3e20ef604f9028f81 Date: Fri, 9 May 2014 20:35:05 -0600 MIME-Version: 1.0 Sent to CCL by: Ronald Cook [cookrl^^tda.com] --20cf301af5d3e20ef604f9028f81 Content-Type: text/plain; charset=UTF-8 Hi Fabio My interests are using Bader's Atom in a Molecules electron density calculations for development of descriptors for QSAR and toxicity studies. I am building a database of molecules for which I first carry out a high level DFT (M06 6311-G+(d,p) calculation and then use Todd Kieths AIIMALL program to carry out the QTAIM calcs. Guassian is the rate limiting step in the process, so I needed several fast but relatively cheap systems so that I could run multiple molecules at the same time. Gaussiam makes it very expensive for non-academics to purchase the parallel versions of Gaussian ($25K). We did a lot of research on computer systems (see the attached excel file). The system I built uses an i7-2700K chip, since this chip as well as a motherboard can be overclocked. In addition to our successes, many other people are routinely getting 5 Ghz from similar setups (you can go as high as 5.4 GHZ but at that level there are too many glitches because of overheating, 5GHz is a nice compromise). Using the i7-2700K gives you a 40% increase from the stock settings of the cheaper 2600K. Of course many 2600k's overclock well also. The higher end simply gives a higher probability that you will get high speeds and a long component lifetime. I have been using this system for three years now Speed measurements are done by taking a benchmark molecule (e.g. an imidazole) running it on our old systems then on the non-overclockedi7-2700K and then on the 5GHz overclocked i7 and noting the cpu time at the end of the Gaussian output file. We have also found that when using the vanilla G09W software that we could get an additional 30% decrease in computational time by doing the following 1 Set up the Gaussian calculation but don't start the calculation process 2 Right click on the task bar on and select task manager and then select processes 3 Right click on g09w and select Set Affinities 4 Uncheck virtual processors 4-7 and hit ok 5 Start your computational run On Fri, May 9, 2014 at 2:49 PM, Fabio cardenas fabiocarden,gmail.com < owner-chemistry * ccl.net> wrote: > Quick two questions, > I am reusing to figure out what I can buy for the money I have. I would > like to build a computer to run Gaussian 09 64 bit. Few calculations > (Fround states, transition states, TDDFT) on organic small molecules. > Does Gaussian uses the hyper threading of intel processors? > For a computer that would be running these calculations for few days, may > be a week non-stop, would a AMD still be OK to buy? Any recommendation on > the hardware I could buy without going for the top of today's technology? > > Thanks > --20cf301af5d3e20ef604f9028f81 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Fabio

My interests are using Bader'= ;s Atom in a Molecules electron density calculations=C2=A0 for development of descriptors for QSAR and=20 toxicity studies.=C2=A0 I am building a database of molecules for which I= =20 first carry out a high level DFT (M06 6311-G+(d,p) calculation and then=20 use Todd Kieths AIIMALL program to carry out the QTAIM calcs.=C2=A0 Guassia= n=20 is the rate limiting step in the process, so I needed several fast but=20 relatively cheap systems so that I could run multiple molecules at the=20 same time. Gaussiam makes it very expensive for non-academics to=20 purchase the parallel versions of Gaussian ($25K).=C2=A0 We did a lot of=20 research on computer systems (see the attached excel file).=C2=A0 The syste= m I built uses an i7-2700K chip, since this chip as well as a=20 motherboard can be overclocked. In=20 addition to our successes, many other people=20 are routinely getting 5 Ghz from similar setups (you can go as high as=20 5.4 GHZ but at that level there are too many glitches because of=20 overheating, 5GHz is a nice compromise).=C2=A0 Using the i7-2700K gives you= a 40%=20 increase from the stock settings of the cheaper 2600K.=C2=A0 Of course many= =20 2600k's overclock well also.=C2=A0 The higher e= nd=20 simply gives a higher probability that you will get high speeds and a long component lifetime.=C2=A0 I have been using this system for three years no= w

Speed measurements are done by taking a benchmark molecule=20 (e.g. an imidazole) running it on our old systems then on the non-overclocked i7-2700K and then on the 5GHz o= verclocked i7 and noting the cpu time at the end of the Gaussian output file.=C2=A0 W= e=20 have also found that when using the vanilla G09W software that we could=20 get an additional 30% decrease in computational time by doing the=20 following

1 Set up the Gaussian calculation but don't start the calculation p= rocess
2 Right click on the task bar on and select task manager and then= select processes
3 Right click on g09w and select Set Affinities
4 Uncheck virtual processors 4-7 and hit ok
5 Start your computational r= un


On Fri, May 9, 2014 at 2:49 PM, Fabio cardenas fabiocarden,gmail.com <owner-chemistry * ccl.net> wrote:
Quick two questions,
I am reusing to fig= ure out what I can buy for the money I have. I would like to build a comput= er to run Gaussian 09 64 bit. Few calculations (Fround states, transition s= tates, TDDFT) on organic small molecules.=C2=A0
Does Gaussian uses the hyper threading = of intel processors?
= For a computer that would be running these=C2=A0calculations for few days,= =C2=A0 may be=C2=A0a week non-stop, would a AMD still be OK to buy? Any rec= ommendation on the hardware I could buy without going for the top of today&= #39;s technology?

Thanks

--20cf301af5d3e20ef604f9028f81-- From owner-chemistry@ccl.net Sat May 10 19:53:00 2014 From: "Moumita Bhattacharya m.bhattacharya]^[aggiemail.usu.edu" To: CCL Subject: CCL:G: Calculation of HOMO-LUMO for a square planar complex of Nickel Message-Id: <-50074-140510174754-16927-vIWXtALq11HKvK9kGOehSg]![server.ccl.net> X-Original-From: Moumita Bhattacharya Content-Type: multipart/alternative; boundary=047d7b34375252392204f912aaa9 Date: Sat, 10 May 2014 15:47:49 -0600 MIME-Version: 1.0 Sent to CCL by: Moumita Bhattacharya [m.bhattacharya#aggiemail.usu.edu] --047d7b34375252392204f912aaa9 Content-Type: text/plain; charset=UTF-8 Hi Brian, Can you tell me how to run the type of calculation you were suggesting? How to start with an initial guess MO? Thank you, Moumita On Fri, May 9, 2014 at 10:20 PM, Moumita Bhattacharya < m.bhattacharya],[aggiemail.usu.edu> wrote: > Hi Brian, > > Thank you for your suggestion. I am using b3lyp basis set and GenECP nosym > gfinput pop=reg iop(6/7=3) keywords for generating the .cub file and I use > the standard orientation, obtained from geometry optimization, in this > input file. I only know this method of finding MO's. > > Thanks, > > Moumita > > > > On Fri, May 9, 2014 at 8:15 PM, Salter-Duke, Brian James > brian.james.duke_-_gmail.com wrote: > >> >> Sent to CCL by: "Salter-Duke, Brian James " [brian.james.duke|| >> gmail.com] >> On Fri, May 09, 2014 at 07:55:28PM -0400, Moumita Bhattacharya >> m.bhattacharya-*-aggiemail.usu.edu wrote: >> > >> > Sent to CCL by: "Moumita Bhattacharya" [m.bhattacharya#%# >> aggiemail.usu.edu] >> > Hello, >> > >> > I am trying to get the HOMO-LUMO of a square planar Ni complex using >> Gaussian. >> > > From my calculation I am getting d(xz) on the Ni contributing as >> HOMO, which is >> > not expected from a square planar complex. I am using the optimized >> geometry >> > for my calculation. Can anyone suggest what should I try differently? >> Isn't it >> > really weird to get d(xz) as the HOMO for sq. pl. geometry? >> >> How did you select you intial guess MOs? It is quite common for the >> algorithms used for the initial guess orbitals to not be the correct MOs >> for the RHF (UHF or ROHF) ground state. However, once selected, they can >> get frozen in so you do not get the correct ground state. You may have >> to swap the inital guess occupied and unoccupied orbitals until you get >> the ones that lead to the lowest energy. >> >> Brian.> >> >> -- >> Brian Salter-Duke (Brian Duke) Brian.Salter-Duke:-:monash.edu >> Adjunct Associate Professor >> Monash Institute of Pharmaceutical Sciences >> Monash University Parkville Campus, VIC 3052, Australia>> >> >> > > > -- > *Moumita Bhattacharya* > *Graduate Student* > *Dept. of Chem & Biochem* > *Utah State University* > *USA* > -- *Moumita Bhattacharya* *Graduate Student* *Dept. of Chem & Biochem* *Utah State University* *USA* --047d7b34375252392204f912aaa9 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Brian,

Can you tell me how to run th= e type of calculation you were suggesting? How to start with an initial gue= ss MO?

Thank you,

Moumita=


On Fri,= May 9, 2014 at 10:20 PM, Moumita Bhattacharya <m.bhattacha= rya],[aggiemail.usu.edu> wrote:
Hi Brian,

Thank you for your suggestion. I am using=C2=A0b3lyp basis set and GenECP= nosym gfinput pop=3Dreg iop(6/7=3D3) keywords for generating the .cub file= and I use the standard orientation, obtained from geometry optimization, i= n this input file. I only know this method of finding MO's.=C2=A0

Thanks,

Moumita

=


On Fri, May 9, 2014 at 8:15 PM, Salter-Duke, Brian Ja= mes brian.james.duke_-_gmail.com <owner-chemistry],[ccl.net>= ; wrote:

Sent to CCL by: "Salter-Duke, Brian James " [brian.james.= duke||gmail.com]
On Fri, May 09, 2014 at 07:55:28PM -0400, Moumita Bhattacharya m.bhatt= acharya-*-aggiemail.= usu.edu wrote:
>
> Sent to CCL by: "Moumita =C2=A0Bhattacharya" [m.bhattacharya= #%#aggiemail.usu.edu= ]
> Hello,
>
> I am trying to get the HOMO-LUMO of a square planar Ni complex using G= aussian.
> > From my calculation I am getting d(xz) on the Ni contributing as = HOMO, which is
> not expected from a square planar complex. I am using the optimized ge= ometry
> for my calculation. Can anyone suggest what should I try differently? = Isn't it
> really weird to get d(xz) as the HOMO for sq. pl. geometry?

How did you select you intial guess MOs? It is quite common for the algorithms used for the initial guess orbitals to not be the correct MOs for the RHF (UHF or ROHF) ground state. However, once selected, they can get frozen in so you do not get the correct ground state. You may have
to swap the inital guess occupied and unoccupied orbitals until you get
the ones that lead to the lowest energy.

Brian.>

--
=C2=A0 =C2=A0Brian Salter-Duke (Brian Duke) =C2=A0 Brian.Salter-Duke:-:monash.edu
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Adjun= ct Associate Professor
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Monash Institute of Pharmaceutica= l Sciences
=C2=A0 =C2=A0 =C2=A0 Monash University Parkville Campus, VIC 3052, Australi= a



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<= /div>--
Moumita Bhattacharya
Graduate Stude= nt
Dept. of Chem = & Biochem
Utah State University
USA



--
Moumita Bhattacharya
Gra= duate Student
Dept. of Chem = & Biochem
Utah State University
USA
--047d7b34375252392204f912aaa9-- From owner-chemistry@ccl.net Sat May 10 21:59:00 2014 From: "Andrew Voronkov drugdesign-*-yandex.ru" To: CCL Subject: CCL: part-time jobs in drug design and chemoinformatics Message-Id: <-50075-140510173226-16092-EYzDy1PlYpuGoNN37fB/BA*o*server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Sun, 11 May 2014 01:32:19 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign[a]yandex.ru] Dear CCL users. are yu aware of any web sites or maybe some freelance web sites, where one may post/find part-time remote jobs in the field of chemoinformatics, molecular modeling and drug design. Best regards, Andrey From owner-chemistry@ccl.net Sat May 10 23:33:00 2014 From: "Jessica Koppen jvkoppen#oakland.edu" To: CCL Subject: CCL: Alternative to WebMO Message-Id: <-50076-140510233116-29347-xgckZ2hr9Lhtwmlv9HKTMg(-)server.ccl.net> X-Original-From: "Jessica Koppen" Date: Sat, 10 May 2014 23:31:15 -0400 Sent to CCL by: "Jessica Koppen" [jvkoppen]=[oakland.edu] Hello everyone ~ Are there any ideas out there in regards to an alternative to WebMO? The constant downloads required due to Java updates has become tedious. Thanks in advance, Jessica Koppen