From owner-chemistry@ccl.net Fri Jul 29 00:03:01 2011 From: "Kalju Kahn kalju-*-chem.ucsb.edu" To: CCL Subject: CCL: Reg: Configuration of a group of computers for Speeding up calculations Message-Id: <-45169-110729000104-7125-BxcFXkHlxfRv3ltCuBHs6g-#-server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 28 Jul 2011 21:00:55 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju()chem.ucsb.edu] Rocky, > Internet connection with pretty good speed (10 Mbs) This is a serious bottleneck, I am afraid. 10 Mbs (10 megabits/s = 1.1 megabytes/sec) speed is all nice for testing the scalability of 32-bit computations on Intel 80386 (the 33.3 MHz version) in a digital electronics lab course, but you want a fatter pipe when running parallel comp chem calculations with i5/i7 processors. Do you realize that modern consumer desktops come with Gigabit Ethernet ports, and that computational nodes in clusters are often connected via aggregate Infiband connections with speeds in the 10 Gbit/s to 40 Gbit/s range? Kalju > Hello Rocky: >   > For your hardware, it is OK. Although not impossible, however, to > construct a cluster by Windows is very awkward, and it is reccommended to > use Linux. > > ---------------------------------------------------------------- > Jun Zhang (coolrainbow(!)yahoo.ch) > Computational Chemistry Group > No.94, Weijinlu > Nankai University > Tianjin, China > > 发件人： rocky walden rocky.walden19-.-gmail.com > > 收件人： "Zhang, Jun " > 发送日期： 2011年7月27日, 星期三, 上午 1:49 > 主题: CCL: Reg: Configuration of a group of computers for Speeding up > calculations > > > Dear CCL folks, > >     I have 3 Laptop machines which operate 24X7 , so i am planning to > group them together and try to make a small group so that i can use them > for exhaustive calculations. > > My lappy configuration. > Intel Dualcore 1.86 GHz,160GB HDD,1GB RAM > Intel Corei7, (quad core) 1.60Ghz, 6GB RAM, 650 GBHDD, 1 GB  Graphics ATI > Mobil radon > Intel Corei5  4GB RAM 350GB,HDD, 512 ATI Radon. > > All these lappys have windows 7 Ultimate OS > > I have license versions of various computational chemistry > (DESMOND,GROMACS, ABINTIO, )suites, can i set up a home cluster ? > Can any one give me some ideas > > > Thanks > Rocky ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Fri Jul 29 06:11:00 2011 From: "Jun Zhang coolrainbow|,|yahoo.cn" To: CCL Subject: CCL: Reg: Configuration of a group of computers for Speeding up calculations Message-Id: <-45170-110729060835-12318-rSgtq134W79uLp9dwoP8Xw*server.ccl.net> X-Original-From: Jun Zhang Content-Type: multipart/alternative; boundary="0-1803052632-1311934104=:41408" Date: Fri, 29 Jul 2011 18:08:24 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: Jun Zhang [coolrainbow[-]yahoo.cn] --0-1803052632-1311934104=:41408 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hello Kahn:=0A=C2=A0=0AThank you for your comment. In my laboratory the clu= ster contains 10 nodes with only gigabit network (1000Mbs), =0Aand the scal= bility is up to only 2 nodes (totally 16 cores). But the speed is sufficien= t for our applications since we have =0Aimplemented GPU accelaration.=0A=C2= =A0=0ACheers up!=0A=C2=A0=0A=0A--------------------------------------------= --------------------=0AJun Zhang (coolrainbow.:.yahoo.ch)=0AComputational Che= mistry Group=0ANo.94, Weijinlu=0ANankai University =0ATianjin, China=0A=0A= =E5=8F=91=E4=BB=B6=E4=BA=BA=EF=BC=9A Kalju Kahn kalju-*-chem.ucsb.edu =0A=E6=94=B6=E4=BB=B6=E4=BA=BA=EF=BC=9A "Zhang, Jun -id= #3zy-" =0A=E5=8F=91=E9=80=81=E6=97=A5=E6=9C=9F=EF=BC= =9A 2011=E5=B9=B47=E6=9C=8829=E6=97=A5, =E6=98=9F=E6=9C=9F=E4=BA=94, =E4=B8= =8B=E5=8D=88 12:00=0A=E4=B8=BB=E9=A2=98: CCL: Reg: Configuration of a group= of computers for Speeding up calculations=0A=0A=0ASent to CCL by: "Kalju K= ahn" [kalju()chem.ucsb.edu]=0ARocky,=0A=0A> Internet connection with pretty= good speed (10 Mbs)=0A=0AThis is a serious bottleneck, I am afraid.=C2=A0 = 10 Mbs (10 megabits/s =3D 1.1=0Amegabytes/sec) speed is all nice for testin= g the scalability of 32-bit=0Acomputations on Intel 80386 (the 33.3 MHz ver= sion) in a digital=0Aelectronics lab course, but you want a fatter pipe whe= n running parallel=0Acomp chem calculations with i5/i7 processors.=0A=0ADo = you realize that modern consumer desktops come with Gigabit Ethernet=0Aport= s, and that computational nodes in clusters are often connected via=0Aaggre= gate Infiband connections with speeds in the 10 Gbit/s to 40 Gbit/s=0Arange= ?=0A=0AKalju=0A=0A> Hello Rocky:=0A> =C2=A0=0A> For your hardware, it is OK= . Although not impossible, however, to=0A> construct a cluster by Windows i= s very awkward, and it is reccommended to=0A> use Linux.=0A>=0A> ----------= ------------------------------------------------------=0A> Jun Zhang (coolr= ainbow(!)yahoo.ch)=0A> Computational Chemistry Group=0A> No.94, Weijinlu=0A= > Nankai University=0A> Tianjin, China=0A>=0A> =E5=8F=91=E4=BB=B6=E4=BA=BA= =EF=BC=9A rocky walden rocky.walden19-.-gmail.com=0A> =0A> =E6=94=B6=E4=BB=B6=E4=BA=BA=EF=BC=9A "Zhang, Jun " =0A> =E5=8F=91=E9=80=81=E6=97=A5=E6=9C=9F=EF=BC=9A 2011=E5=B9=B4= 7=E6=9C=8827=E6=97=A5, =E6=98=9F=E6=9C=9F=E4=B8=89, =E4=B8=8A=E5=8D=88 1:49= =0A> =E4=B8=BB=E9=A2=98: CCL: Reg: Configuration of a group of computers fo= r Speeding up=0A> calculations=0A>=0A>=0A> Dear CCL folks,=0A>=0A> =C2=A0= =C2=A0=C2=A0 I have 3 Laptop machines which operate 24X7 , so i am planning= to=0A> group them together and try to make a small group so that i can use= them=0A> for exhaustive calculations.=0A>=0A> My lappy configuration.=0A> = Intel Dualcore 1.86 GHz,160GB HDD,1GB RAM=0A> Intel Corei7, (quad core) 1.6= 0Ghz, 6GB RAM, 650 GBHDD, 1 GB=C2=A0 Graphics ATI=0A> Mobil radon=0A> Intel= Corei5=C2=A0 4GB RAM 350GB,HDD, 512 ATI Radon.=0A>=0A> All these lappys ha= ve windows 7 Ultimate OS=0A>=0A> I have license versions of various computa= tional chemistry=0A> (DESMOND,GROMACS, ABINTIO, )suites, can i set up a hom= e cluster ?=0A> Can any one give me some ideas=0A>=0A>=0A> Thanks=0A> Rocky= =0A=0A=0A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~=0ADr. Kalju Kahn=0ADepartment of= Chemistry and Biochemistry=0AUC Santa Barbara, CA 93106=0A=0A=0A=0A-=3D Th= is is automatically added to each message by the mailing script =3D-=0ATo r= ecover the email address of the author of the message, please change=0Athe = strange characters on the top line to the .:. sign. You can also=0Alook up th= e X-Original-From: line in the mail header.=0A=0AE-mail to subscribers: CHE= MISTRY.:.ccl.net or use:=0A=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/cc= l/send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-REQUEST.:.ccl.net= or use=0A=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_mess= age=0A=0A=0A=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/= chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait time at: http://w= ww.ccl.net=0A=0A=0AConferences: http://server.= ccl.net/chemistry/announcements/conferences/=0A=0ASearch Messages: http://w= ww.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail bounces from C= CL with 5.7.1 error, check:=0A=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spamm= ers.txt=0A=0A--0-1803052632-1311934104=:41408 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hello Kahn= :
 
Thank you for your c= omment. In my laboratory the cluster contains 10 nodes with o<= /span>nly gigabit network (1000Mbs),
and the = scalbility is up to only 2 nodes (totally 16 cores). But the speed is suffi= cient for our applications since we have
implemente= d GPU accelaration.
 
Ch= eers up!
&nbs= p;
 
----------------------------------= ------------------------------
Jun Zhang (coolrainbow.:.yahoo.ch)
Compu= tational Chemistry Group
No.94, Weijinlu
Nankai University
Tianji= n, China
=E5=8F=91=E4=BB=B6=E4=BA=BA=EF=BC=9A Kalju Kahn kalju-*-ch= em.ucsb.edu <owner-chemistry.:.ccl.net>
=E6=94=B6=E4=BB=B6=E4=BA=BA=EF=BC=9A "Zhang, Jun -id#3= zy-" <coolrainbow.:.yahoo.cn>
= =E5=8F=91=E9=80=81=E6=97=A5=E6=9C=9F=EF=BC=9A 2011=E5=B9=B47=E6= =9C=8829=E6=97=A5, =E6=98=9F=E6=9C=9F=E4=BA=94, =E4=B8=8B=E5=8D=88 12:00=E4=B8=BB=E9=A2=98: CCL: = Reg: Configuration of a group of computers for Speeding up calculations
=

Sent to CCL by: "Kalju Kahn" [kalju()chem.ucsb.edu]
Rocky= ,

> Internet connection with pretty good speed (10 Mbs)

Th= is is a serious bottleneck, I am afraid.  10 Mbs (10 megabits/s =3D 1.1<= br>megabytes/sec) speed is all nice for testing the scalability of 32-bitcomputations on Intel 80386 (the 33.3 MHz version) in a digital
electr= onics lab course, but you want a fatter pipe when running parallel
comp = chem calculations with i5/i7 processors.

Do you realize that modern = consumer desktops come with Gigabit Ethernet
ports, and that computation= al nodes in clusters are often connected via
aggregate Infiband connecti= ons with speeds in the 10 Gbit/s to 40 Gbit/s
range?

Kalju
> Hello Rocky:
>  
> For your hardware, it is OK. Alth= ough not impossible, however, to
> construct a cluster by Windows is = very awkward, and it is reccommended to
> use Linux.
>
> = ----------------------------------------------------------------
> Ju= n Zhang (coolrainbow(!)yahoo.ch)
> Computational Chemistry Group
> No.94, Weijinlu
> Nankai University
> Tianjin, C= hina
>
> =E5=8F=91=E4=BB=B6=E4=BA=BA=EF=BC=9A rocky walden rock= y.walden19-.-gmail.com
> <owner-chemistry(!)ccl.net>
> = =E6=94=B6=E4=BB=B6=E4=BA=BA=EF=BC=9A "Zhang, Jun " <coolrainbow(!)yahoo.= cn>
> =E5=8F=91=E9=80=81=E6=97=A5=E6=9C=9F=EF=BC=9A 2011=E5=B9=B47= =E6=9C=8827=E6=97=A5, =E6=98=9F=E6=9C=9F=E4=B8=89, =E4=B8=8A=E5=8D=88 1:49<= br>> =E4=B8=BB=E9=A2=98: CCL: Reg: Configuration of a group of computers= for Speeding up
> calculations
>
>
> Dear CCL folk= s,
>
>     I have 3 Laptop machines which operat= e 24X7 , so i am planning to
> group them together and try to make a = small group so that i can use them
> for exhaustive calculations.
= >
> My lappy configuration.
> Intel Dualcore 1.86 GHz,160GB = HDD,1GB RAM
> Intel Corei7, (quad core) 1.60Ghz, 6GB RAM, 650 GBHDD, = 1 GB  Graphics ATI
> Mobil radon
> Intel Corei5  4GB = RAM 350GB,HDD, 512 ATI Radon.
>
> All these lappys have windows 7 Ultimate OS
>
> I have license versions = of various computational chemistry
> (DESMOND,GROMACS, ABINTIO, )suit= es, can i set up a home cluster ?
> Can any one give me some ideas>
>
> Thanks
> Rocky


~~~~~~~~~~~~~~~~~~~~~= ~~~~~~~~~~~~
Dr. Kalju Kahn
Department of Chemistry and Biochemistry<= br>UC Santa Barbara, CA 93106



-=3D This is automatically add= ed to each message by the mailing script =3D-
To recover the email addre= ss of the author of the message, please change
the strange characters on= the top line to the .:. sign. You can also
look up the X-Original-From: l= ine in the mail header.

E-mail to subscribers: CHEMISTRY.:.ccl.net = or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message
<= br>E-mail to administrators: CHEMISTRY-REQUEST.:.ccl.net o= r use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_me= ssage
      http://www= .ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait ti= me at: http://www.ccl.net<= /a>

Job: http:= //www.ccl.net/jobs
Conferences: http://server.ccl.net= /chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml

If your m= ail bounces from CCL with 5.7.1 error, check:
      http://www.ccl.net= /spammers.txt

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




--0-1803052632-1311934104=:41408-- From owner-chemistry@ccl.net Fri Jul 29 08:14:01 2011 From: "Leonid Shirkov leonid.shirkov%a%tiger.chem.uw.edu.pl" To: CCL Subject: CCL:G: different basis functions for different atoms in gaussian Message-Id: <-45171-110729081238-19486-GwDn8pSRaDddsS66IGBOgQ : server.ccl.net> X-Original-From: "Leonid Shirkov" Date: Fri, 29 Jul 2011 08:12:36 -0400 Sent to CCL by: "Leonid Shirkov" [leonid.shirkov**tiger.chem.uw.edu.pl] Dear Colleagues, I need to calculate interaction energies of Van der Waals complexes in Gaussian 03 (or 09) and I need to introduce special basis set for the midbond functions. So, my questions are: 1) How to use different basis sets for different atoms in Gaussian? 2) How to define the following basis set [3s3p2d1f1g]? This one I need to use for the midbond. Thank you in advance, Leonid Shirkov From owner-chemistry@ccl.net Fri Jul 29 08:49:01 2011 From: "Sanjay Bharathwaj computationalchemist+*+gmail.com" To: CCL Subject: CCL: Molecular Formula to Structures - Free ware Message-Id: <-45172-110729051340-31637-lTsMYQoAM2VKBrgMBTZFdw!=!server.ccl.net> X-Original-From: Sanjay Bharathwaj Content-Type: multipart/alternative; boundary=001636c92c621283c004a931b294 Date: Fri, 29 Jul 2011 11:13:32 +0200 MIME-Version: 1.0 Sent to CCL by: Sanjay Bharathwaj [computationalchemist,,gmail.com] --001636c92c621283c004a931b294 Content-Type: text/plain; charset=ISO-8859-1 Dear Colleagues, I am looking for a program (free ware/or with full trial version for limited time) that can list the possible structures (organometallic compound) when the molecular formula is given. For example i know for organic molecules MOLGEN does this job. But that's not free as well. (molgen(dot)de) If you have any kind of codes/genetic algorithm that can do this job, please share your knowledge and your help will be acknowledged suitably. Best regards, Dr. Sanjay -- Regards, Dr. Sanjay Bharathwaj Kumar, Dharmendra Institute of Technology, India. --001636c92c621283c004a931b294 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear=A0Colleagues,

=
I am looking for a=A0program (free ware/or with full trial version for= limited time)=A0that can list the possible structures
(organometallic compound) when the molecular=A0formula=A0is given.

For example i know for organic molecules MOLGEN does = this job.
But that's not free as well. (molgen(dot)de)
<= div>
If you have any kind of codes/genetic algorithm that can do = this=A0
job, please share your knowledge and your help will be ac= knowledged=A0
suitably.

Best regards,
Dr. Sanjay

--
Regards,
Dr. Sanjay B= harathwaj Kumar,
Dharmendra Institute of Technology,
India.
--001636c92c621283c004a931b294-- From owner-chemistry@ccl.net Fri Jul 29 10:20:00 2011 From: "Abhik Seal abhik1368*_*gmail.com" To: CCL Subject: CCL: Molecular Formula to Structures - Free ware Message-Id: <-45173-110729100754-10126-1bojRE2fpkUNTGJFta6bOw---server.ccl.net> X-Original-From: Abhik Seal Content-Type: multipart/alternative; boundary=20cf303f6dfa3be6e204a935ced6 Date: Fri, 29 Jul 2011 19:37:25 +0530 MIME-Version: 1.0 Sent to CCL by: Abhik Seal [abhik1368*o*gmail.com] --20cf303f6dfa3be6e204a935ced6 Content-Type: text/plain; charset=ISO-8859-1 Hi Why dont you use online tool http://cactus.nci.nih.gov/chemical/structure and you can also use Opsin (http://opsin.ch.cam.ac.uk/) to thank you Abhik Seal *OSDD CHEMINFORMATICS* +919831682877 http://osddcheminfo.webs.com On Fri, Jul 29, 2011 at 2:43 PM, Sanjay Bharathwaj computationalchemist+*+ gmail.com wrote: > Dear Colleagues, > > I am looking for a program (free ware/or with full trial version for > limited time) that can list the possible structures > (organometallic compound) when the molecular formula is given. > > For example i know for organic molecules MOLGEN does this job. > But that's not free as well. (molgen(dot)de) > > If you have any kind of codes/genetic algorithm that can do this > job, please share your knowledge and your help will be acknowledged > suitably. > > Best regards, > Dr. Sanjay > > -- > Regards, > Dr. Sanjay Bharathwaj Kumar, > Dharmendra Institute of Technology, > India. > --20cf303f6dfa3be6e204a935ced6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi=A0

Why dont you use online tool=A0http://cactus.nci.nih.gov/chemical/st= ructure=A0 and you can also use Opsin (http://opsin.ch.cam.ac.uk/) to=A0

thank you=A0
=A0
Abhik Seal
OSDD CHEMINFORMATICS
+91983168= 2877
http://osddchem= info.webs.com



On Fri, Jul 29, 2011 at 2:43 PM, Sanjay = Bharathwaj computationalchemist+*+gmail.com <owner-ch= emistry ~~ ccl.net> wrote:
Dear=A0Colleagues,

=
I am looking for a=A0program (free ware/or with full trial version for limi= ted time)=A0that can list the possible structures
(organometallic compound) when the molecular=A0formula=A0is given.

For example i know for organic molecules MOLGEN does = this job.
But that's not free as well. (molgen(dot)de)

If you have any kind of codes/genetic algorithm that can do = this=A0
job, please share your knowledge and your help will be ac= knowledged=A0
suitably.

Best regards,
Dr. Sanjay

--
= Regards,
Dr. Sanjay Bharathwaj Kumar,
Dharmendra Institute of Technol= ogy,
India.

--20cf303f6dfa3be6e204a935ced6-- From owner-chemistry@ccl.net Fri Jul 29 14:12:00 2011 From: "Wolf Ihlenfeldt wdi++xemistry.com" To: CCL Subject: CCL: Molecular Formula to Structures - Free ware Message-Id: <-45174-110729114640-24852-hzIxGyDCgf9yOJov+7Aikw_-_server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Type: multipart/alternative; boundary=bcaec520ede3824f6104a9372f92 Date: Fri, 29 Jul 2011 17:46:32 +0200 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi(0)xemistry.com] --bcaec520ede3824f6104a9372f92 Content-Type: text/plain; charset=UTF-8 I do not think this is what Sanjay needs. This post is not helpful. On Fri, Jul 29, 2011 at 4:07 PM, Abhik Seal abhik1368*_*gmail.com < owner-chemistry{=}ccl.net> wrote: > Hi > > Why dont you use online tool http://cactus.nci.nih.gov/chemical/structure > and you can also use Opsin (http://opsin.ch.cam.ac.uk/) to > > thank you > > Abhik Seal > *OSDD CHEMINFORMATICS* > +919831682877 > http://osddcheminfo.webs.com > > > > On Fri, Jul 29, 2011 at 2:43 PM, Sanjay Bharathwaj computationalchemist+*+ > gmail.com wrote: > >> Dear Colleagues, >> >> I am looking for a program (free ware/or with full trial version for >> limited time) that can list the possible structures >> (organometallic compound) when the molecular formula is given. >> >> For example i know for organic molecules MOLGEN does this job. >> But that's not free as well. (molgen(dot)de) >> >> If you have any kind of codes/genetic algorithm that can do this >> job, please share your knowledge and your help will be acknowledged >> suitably. >> >> Best regards, >> Dr. Sanjay >> >> -- >> Regards, >> Dr. Sanjay Bharathwaj Kumar, >> Dharmendra Institute of Technology, >> India. >> > > -- Wolf-D. Ihlenfeldt, Xemistry GmbH www.xemistry.com --bcaec520ede3824f6104a9372f92 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
I do not think this is what Sanjay needs. This post is not helpful.
=
On Fri, Jul 29, 2011 at 4:07 PM, Abhik Seal = abhik1368*_*gmail.com &l= t;owner-chemistry{=}ccl.net>= ; wrote:
Hi=C2=A0

=
Why dont you use online tool=C2=A0http://cactus.nci.nih.gov/chem= ical/structure=C2=A0 and you can also use Opsin (http://opsin.ch.cam.ac.uk/) to=C2=A0=

thank you=C2=A0
=C2=A0
Abhik Seal
OSDD CHEMINFORMATICS
+919= 831682877
http://osddchem= info.webs.com



On Fri, Jul 29, 2011 at 2:43 PM, Sanjay = Bharathwaj computationalchemist+*+gmail.com <owner-chemistry,ccl.net> wrote:
D= ear=C2=A0Colleagues,

I am looking for a=C2=A0program (free ware/or with full trial version for l= imited time)=C2=A0that can list the possible structures
(organometallic compound) when the molecular=C2=A0formula=C2=A0is give= n.

For example i know for organic molecules MOLGEN= does this job.
But that's not free as well. (molgen(dot)de)<= /div>

If you have any kind of codes/genetic algorithm that can do = this=C2=A0
job, please share your knowledge and your help will be= acknowledged=C2=A0
suitably.

Best regar= ds,
Dr. Sanjay

--
= Regards,
Dr. Sanjay Bharathwaj Kumar,
Dharmendra Institute of Technol= ogy,
India.




--
Wolf-D. Ihlenfeldt, Xem= istry GmbH
www.xem= istry.com

--bcaec520ede3824f6104a9372f92-- From owner-chemistry@ccl.net Fri Jul 29 20:05:01 2011 From: "Kadir Diri dirikadir!^!gmail.com" To: CCL Subject: CCL: Charge - Accuracy Message-Id: <-45175-110728203555-11728-DPaXH9MIEG7pNEV28c+ujA.@.server.ccl.net> X-Original-From: Kadir Diri Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 28 Jul 2011 17:35:15 -0700 MIME-Version: 1.0 Sent to CCL by: Kadir Diri [dirikadir#,#gmail.com] Hi Eliac, You can also check higher moments, not just dipole, and compare with accurate electronic structure or experimental values. In addition, you can try benchmarking against some well-established charge calculation methods. Charge is not a quantum mechanical observable, so any charge calculation will be sort of arbitrary, but it is known that some methods are better than others, in general. For example NBO has a strong physical motivation and for well-behaved molecules, it may make sense to compare against. Cheers! kadir On 07/25/2011 02:42 AM, Eliac Brown Eliacbrown],[yahoo.com wrote: > Sent to CCL by: "Eliac Brown" [Eliacbrown- -yahoo.com] > Dear ALL > I calculated the atomic partial charges for my small molecule using two > different methods. The two methods generated charges so close to each other. > I want to test the accuracy of the generated charges of the two tested methods > and compare to each other, to select the best method of charge calculation. > I studied dipolemoment and interaction energy (with substrates) of the > molecule. > I was wondering what other criteria/properties/calculation should I test to > evaluate the generated charges. > All the calculations are molecular mechanical using AMBER > Thanks, Eliac > --------------- Kadir Diri, PhD Research Scientist Department of Chemistry and iOpenShell Center SSC #401 University of Southern California Los Angeles, CA 90089-0482 www:http://iopenshell.usc.edu/kadir -------------------------- Relativistic correction to Murphy's law: Whether things can go wrong or not, depends on your frame of reference. From owner-chemistry@ccl.net Fri Jul 29 20:39:01 2011 From: "Eustis Soren soren.eustis^_^env.ethz.ch" To: CCL Subject: CCL: Spin-Orbit Coupling Message-Id: <-45176-110729194940-11975-4VcqPwsuMzSIxtRy8SKCoQ _ server.ccl.net> X-Original-From: "Eustis Soren" Content-ID: <37CC584F2E3EBE4A98EDBF2D23D30ACB _ intern.ethz.ch> Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Fri, 29 Jul 2011 23:49:29 +0000 MIME-Version: 1.0 Sent to CCL by: "Eustis Soren" [soren.eustis{=}env.ethz.ch] Greetings. I am interested in determining the differences in spin-orbit coupling, and more specifically the rate of intersystem crossing (S1-T1) for two seperate heterocycles containing different isotopes of nitrogen. It seems that there are a few codes which can model this, but I am not entirely comfortable with the implementation. Does anyone have experience with this area of research? I would appreciate any suggestions or references. Regards, Soren Soren N. Eustis, Ph.D. ETH Zrich Environmental Chemistry Group Institute for Biogeochemistry and Pollutant Dynamics Universittstrasse 16 CHN F33 8092 Zrich SWITZERLAND +41 44 632 93 48 (office) +41 44 632 14 38 (fax) soren*|*env.ethz.ch