From owner-chemistry@ccl.net Mon May 27 05:38:00 2013 From: "WuChaofu xiaowu759*o*hotmail.com" To: CCL Subject: CCL: How to characterize and change the tacticity of polymer chain Message-Id: <-48734-130527053226-19877-65ssfyq1rOmbiW1KQQZ0oQ=-=server.ccl.net> X-Original-From: WuChaofu Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 27 May 2013 17:32:17 +0800 MIME-Version: 1.0 Sent to CCL by: WuChaofu [xiaowu759=-=hotmail.com] Dear CCLers, I have an atomistic model (pdb file), which is an isotactic polymer chain. From the visualized model, I can tell the tacticity.  However, how to characterize the tacticity using some geometric parameters (i.e., bond angles, dihedral angles)? And how to change the tacticity from isotactic to syndiotactic by some geometric operations? Thanks a lot for any reply to this letter. Yours sincerely, Chaofu Wu From owner-chemistry@ccl.net Mon May 27 07:02:01 2013 From: "Michel Petitjean petitjean.chiral * gmail.com" To: CCL Subject: CCL: How to characterize and change the tacticity of polymer chain Message-Id: <-48735-130527065859-31541-BEMFt2Tywl98zxlaI/Z2OQ(_)server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 27 May 2013 12:58:49 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral\a/gmail.com] Dear Chaofu, Even for one asymmetric carbon it is hard to build a program implementing the CIP rules working in any case (in fact the CIP rules do not work in any case), and even recognizing an asymmetric carbon can be hard: the main difficulty is to check when two substituents are different or not. For a specific class of polymers, a simplified analysis to locate the stereocenters and prioritize the substituents should be easier. Once done, flagging the polymer as isotactic or syndiotactic or none of them is easy, even if you use some house defined priority rules rather than the CIP ones. In any case, once the asymmetric carbon is recognized and once its four substituents 1<2<3<4 are prioritized, you may perform as follows: (1) put the carbon at the origin, (2) check if the centered trihedron 2->3->4 is direct or not (i.e. compute the sign of the determinant [2,3,4]), (3) assign the desired stereo flag. Isotactic/syndiotactic analysis reduces to check the sequence of flags. Hope it helps. Best, Michel. Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral**gmail.com (preferred), michel.petitjean**univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html 2013/5/27 WuChaofu xiaowu759*o*hotmail.com : > > Sent to CCL by: WuChaofu [xiaowu759=-=hotmail.com] > Dear CCLers, > I have an atomistic model (pdb file), which is an isotactic polymer chain. From the visualized model, I can tell the tacticity. However, how to characterize the tacticity using some geometric parameters (i.e., bond angles, dihedral angles)? And how to change the tacticity from isotactic to syndiotactic by some geometric operations? Thanks a lot for any reply to this letter. > Yours sincerely, > Chaofu Wu > From owner-chemistry@ccl.net Mon May 27 10:17:00 2013 From: "Shireen Alfalah shireenfalah/./hotmail.com" To: CCL Subject: CCL: Server qualities Message-Id: <-48736-130527053107-19780-ZdRZW+5ALqi1taBpviT/TQ=-=server.ccl.net> X-Original-From: Shireen Alfalah Content-Type: multipart/alternative; boundary="_3b4a401a-8acf-45ca-b458-0a7398150ef0_" Date: Mon, 27 May 2013 11:31:00 +0200 MIME-Version: 1.0 Sent to CCL by: Shireen Alfalah [shireenfalah|,|hotmail.com] --_3b4a401a-8acf-45ca-b458-0a7398150ef0_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Johannes=2C Not at all. On the contrary I appreciate your kind advice = as well as any other kind advice. It is completely understandable that diff= erent people would have different experience and accordingly different opin= ions and I am looking forward to know about them if any one wants to share = his kind experience. I am very grateful for your kind advice and sharing yo= ur experience with us. Many thanks for your precious advises!!!Kind regards= Sherin Alfalah=20 > From: owner-chemistry~~ccl.net > To: shireenfalah~~hotmail.com > Subject: CCL: Server qualities > Date: Sun=2C 26 May 2013 19:58:51 -0400 >=20 >=20 > Sent to CCL by: "Johannes Hachmann" [jh~~chemistry.harvard.edu] > Dear Sherin=2C >=20 > I received an off-list eMail with a rather stiff blowback on my previous > note which made me realize that I should have been more careful in my > formulation.=20 >=20 > First=2C let me stress that I don't have any direct or indirect stake > whatsoever (financial or otherwise) in Dell or any other hardware company= =2C > nor do I have an agenda on the topic of hardware. My eMail was not a form= al > endorsement or advertisement of any kind=2C and I did not mean to suggest= that > the hardware I mentioned is better than its competitors. I only wanted to > share my personal experience - for whatever that's worth. If this intenti= on > was misunderstood I sincerely apologize! =20 >=20 > It was suggested that my opinion is biased and that is indeed the case > because I know the R420/R620 and the similar C6100/C6220 series. I've bee= n > happy with both (although it was explained to me that the latter actually > has a substandard RAID controller and I/O performance)=2C which I cannot = claim > for all clusters I used. =20 >=20 > I also appreciate the responsiveness of the Dell reps in for quotes and > customization requests (although my latest contact was subpar)=2C the pri= cing > seems fair=2C the professional sys admins I talk to in two academic rese= arch > computing centers seem to like the Dells (although they use a wide > assortment of other hardware as well). The centers I'm familiar with have > thousands of cores in these systems. So=2C for whatever anecdotal evidenc= e is > worth=2C this suggestion at least does not seem farfetched. >=20 > The biggest criticism I received was regarding bad business=2C labor=2C > environmental=2C and customer practices by Dell. I personally had only > positive experience with respect to the last point (both for > high-performance computing and personal laptops I used to have). I really > have no idea whether Dell is particularly bad with respect to labor=2C > environment=2C and business practices - my impression is that all the big > companies produce in the same Foxconn facility in China and are equally > guilty of dubious behavior. But I may well be wrong on this.=20 >=20 > I would very much appreciate to hear of people's less positive experience > with the mentioned hardware - I'm always happy to learn. >=20 > For the time being I wanted to mention a system which I don't know first > hand=2C but I like the idea and admire the scientist behind it:=20 > http://pqs-chem.com/=20 > Maybe that's the right computer for you. >=20 > Here is another resource that may be helpful in your search:=20 > http://www.siliconmechanics.com/ >=20 > Best wishes and my apologies for any irritations I may have caused earlie= r=2C >=20 > Johannes=20 >=20 >=20 > ----------------------------------------------- > Dr. Johannes Hachmann > Research Associate > Harvard University > Department of Chemistry and Chemical Biology > 12 Oxford St=2C Rm M104A > Cambridge=2C MA 02138 > ----------------------------------------------- >=20 >=20 > > -----Original Message----- > > From: owner-chemistry+jh=3D=3Dchemistry.harvard.edu(-)ccl.net [mailto:o= wner- > > chemistry+jh=3D=3Dchemistry.harvard.edu(-)ccl.net] On Behalf Of Johanne= s > > Hachmann jh|-|chemistry.harvard.edu > > Sent: Sunday=2C 26 May=2C 2013 11:49 > > To: Hachmann=2C Johannes=20 > > Subject: CCL: Server qualities > >=20 > >=20 > > Sent to CCL by: "Johannes Hachmann" [jh=2C+=2Cchemistry.harvard.edu] Hi > Sherin=2C > >=20 > > Such a purchase decision very much depends on what kind of studies you > want > > to do=2C but (without wanting to make undue advertisement) the Dell > R420/R620 > > chassis is a pretty good design and value=2C in particular if you alrea= dy > have a > > suitable rack. Then you can fit the nodes with the CPUs=2C RAM=2C IB et= c > according > > to your needs. Again=2C this is just one solution which happens to > > work well for quantum chemistry but there are many others. > >=20 > > Best > >=20 > > Johannes > >=20 > > ----------------------------------------------- > > Dr. Johannes Hachmann > > Research Associate > > Harvard University > > Department of Chemistry and Chemical Biology > > 12 Oxford St=2C Rm M104A > > Cambridge=2C MA 02138 > > ----------------------------------------------- > >=20 > >=20 > >=20 > > > -----Original Message----- > > > From: owner-chemistry+jh=3D=3Dchemistry.harvard.edu-$-ccl.net > > > [mailto:owner- > > > chemistry+jh=3D=3Dchemistry.harvard.edu-$-ccl.net] On Behalf Of Sheri= n > > > chemistry+Alfalah > > > shireen.alfalah]=2C[yahoo.com > > > Sent: Sunday=2C 26 May=2C 2013 04:47 > > > To: Hachmann=2C Johannes > > > Subject: CCL: Server qualities > > > > > > > > > Sent to CCL by: "Sherin Alfalah" [shireen.alfalah-=2C-yahoo.com] > > > Dear CCL users=2C > > > I am wondering if I can have a kind advice on the qualifications of a > > server that > > > is supposed to run molecular or quantum chemistry calculations for > > > systems constituted of 60-70 atoms. The server is planned to be used > > > by 5 or 6 > > users. > > > Thank you very much for your precious advice. > > > Best regards > > > Sherin AlfalahTo > > > recover the email address of the author of the message=2C please chan= ge > > > the strange characters on the top line to the -$- sign. You can also > > > look up the > > X- > > > Original-From: line in the mail header.To > > recover the email address of the author of the message=2C please change= the > > strange characters on the top line to the (-) sign. You can also look u= p the > X- > > Original-From: line in the mail header. >=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=2C please chang= e>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20 > Before posting=2C check wait time at: http://www.ccl.net >=20 > Job: http://www.ccl.net/jobs=20>=20>=20 > If your mail bounces from CCL with 5.7.1 error=2C check:>=20>=20 >=20 = --_3b4a401a-8acf-45ca-b458-0a7398150ef0_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear =3BJohannes=2C =3B<= div>Not at all. On the contrary I appreciate your kind advice as well as an= y other kind advice. =3B
It is completely understandable that= different people would have different experience and accordingly different= opinions and I am looking forward to know about them if any one wants to s= hare his kind experience. =3B
I am very grateful for your kin= d advice and sharing your experience with us. =3B
Many thanks= for your precious advises!!!
= Kind regards =3B
Sh= erin Alfalah =3B



>=3B Fr= om: owner-chemistry~~ccl.net
>=3B To: shireenfalah~~hotmail.com
>= =3B Subject: CCL: Server qualities
>=3B Date: Sun=2C 26 May 2013 19:58= :51 -0400
>=3B
>=3B
>=3B Sent to CCL by: "Johannes Hachman= n" [jh~~chemistry.harvard.edu]
>=3B Dear Sherin=2C
>=3B
>= =3B I received an off-list eMail with a rather stiff blowback on my previou= s
>=3B note which made me realize that I should have been more careful= in my
>=3B formulation.
>=3B
>=3B First=2C let me stress = that I don't have any direct or indirect stake
>=3B whatsoever (financ= ial or otherwise) in Dell or any other hardware company=2C
>=3B nor do= I have an agenda on the topic of hardware. My eMail was not a formal
&g= t=3B endorsement or advertisement of any kind=2C and I did not mean to sugg= est that
>=3B the hardware I mentioned is better than its competitors.= I only wanted to
>=3B share my personal experience - for whatever tha= t's worth. If this intention
>=3B was misunderstood I sincerely apolog= ize!
>=3B
>=3B It was suggested that my opinion is biased and= that is indeed the case
>=3B because I know the R420/R620 and the sim= ilar C6100/C6220 series. I've been
>=3B happy with both (although it w= as explained to me that the latter actually
>=3B has a substandard RAI= D controller and I/O performance)=2C which I cannot claim
>=3B for all= clusters I used.
>=3B
>=3B I also appreciate the responsivene= ss of the Dell reps in for quotes and
>=3B customization requests (alt= hough my latest contact was subpar)=2C the pricing
>=3B seems fair=2C = the professional sys admins I talk to in two academic research
>=3B c= omputing centers seem to like the Dells (although they use a wide
>=3B= assortment of other hardware as well). The centers I'm familiar with have<= br>>=3B thousands of cores in these systems. So=2C for whatever anecdotal= evidence is
>=3B worth=2C this suggestion at least does not seem farf= etched.
>=3B
>=3B The biggest criticism I received was regarding= bad business=2C labor=2C
>=3B environmental=2C and customer practices= by Dell. I personally had only
>=3B positive experience with respect = to the last point (both for
>=3B high-performance computing and person= al laptops I used to have). I really
>=3B have no idea whether Dell is= particularly bad with respect to labor=2C
>=3B environment=2C and bus= iness practices - my impression is that all the big
>=3B companies pro= duce in the same Foxconn facility in China and are equally
>=3B guilty= of dubious behavior. But I may well be wrong on this.
>=3B
>= =3B I would very much appreciate to hear of people's less positive experien= ce
>=3B with the mentioned hardware - I'm always happy to learn.
&g= t=3B
>=3B For the time being I wanted to mention a system which I don= 't know first
>=3B hand=2C but I like the idea and admire the scientis= t behind it:
>=3B http://pqs-chem.com/
>=3B Maybe that's the ri= ght computer for you.
>=3B
>=3B Here is another resource that ma= y be helpful in your search:
>=3B http://www.siliconmechanics.com/>=3B
>=3B Best wishes and my apologies for any irritations I may h= ave caused earlier=2C
>=3B
>=3B Johannes
>=3B
>=3B <= br>>=3B -----------------------------------------------
>=3B Dr. Joh= annes Hachmann
>=3B Research Associate
>=3B Harvard University>=3B Department of Chemistry and Chemical Biology
>=3B 12 Oxford St= =2C Rm M104A
>=3B Cambridge=2C MA 02138
>=3B --------------------= ---------------------------
>=3B
>=3B
>=3B >=3B -----Ori= ginal Message-----
>=3B >=3B From: owner-chemistry+jh=3D=3Dchemistry= .harvard.edu(-)ccl.net [mailto:owner-
>=3B >=3B chemistry+jh=3D=3Dch= emistry.harvard.edu(-)ccl.net] On Behalf Of Johannes
>=3B >=3B Hachm= ann jh|-|chemistry.harvard.edu
>=3B >=3B Sent: Sunday=2C 26 May=2C 2= 013 11:49
>=3B >=3B To: Hachmann=2C Johannes
>=3B >=3B Subje= ct: CCL: Server qualities
>=3B >=3B
>=3B >=3B
>=3B >= =3B Sent to CCL by: "Johannes Hachmann" [jh=2C+=2Cchemistry.harvard.edu] Hi=
>=3B Sherin=2C
>=3B >=3B
>=3B >=3B Such a purchase dec= ision very much depends on what kind of studies you
>=3B want
>= =3B >=3B to do=2C but (without wanting to make undue advertisement) the D= ell
>=3B R420/R620
>=3B >=3B chassis is a pretty good design an= d value=2C in particular if you already
>=3B have a
>=3B >=3B s= uitable rack. Then you can fit the nodes with the CPUs=2C RAM=2C IB etc
= >=3B according
>=3B >=3B to your needs. Again=2C this is just one = solution which happens to
>=3B >=3B work well for quantum chemistry = but there are many others.
>=3B >=3B
>=3B >=3B Best
>= =3B >=3B
>=3B >=3B Johannes
>=3B >=3B
>=3B >=3B --= ---------------------------------------------
>=3B >=3B Dr. Johannes= Hachmann
>=3B >=3B Research Associate
>=3B >=3B Harvard Univ= ersity
>=3B >=3B Department of Chemistry and Chemical Biology
>= =3B >=3B 12 Oxford St=2C Rm M104A
>=3B >=3B Cambridge=2C MA 02138<= br>>=3B >=3B -----------------------------------------------
>=3B = >=3B
>=3B >=3B
>=3B >=3B
>=3B >=3B >=3B -----Or= iginal Message-----
>=3B >=3B >=3B From: owner-chemistry+jh=3D=3Dc= hemistry.harvard.edu-$-ccl.net
>=3B >=3B >=3B [mailto:owner-
&g= t=3B >=3B >=3B chemistry+jh=3D=3Dchemistry.harvard.edu-$-ccl.net] On Be= half Of Sherin
>=3B >=3B >=3B chemistry+Alfalah
>=3B >=3B &= gt=3B shireen.alfalah]=2C[yahoo.com
>=3B >=3B >=3B Sent: Sunday=2C= 26 May=2C 2013 04:47
>=3B >=3B >=3B To: Hachmann=2C Johannes
&= gt=3B >=3B >=3B Subject: CCL: Server qualities
>=3B >=3B >=3B<= br>>=3B >=3B >=3B
>=3B >=3B >=3B Sent to CCL by: "Sherin A= lfalah" [shireen.alfalah-=2C-yahoo.com]
>=3B >=3B >=3B Dear CCL us= ers=2C
>=3B >=3B >=3B I am wondering if I can have a kind advice o= n the qualifications of a
>=3B >=3B server that
>=3B >=3B >= =3B is supposed to run molecular or quantum chemistry calculations for
&= gt=3B >=3B >=3B systems constituted of 60-70 atoms. The server is plann= ed to be used
>=3B >=3B >=3B by 5 or 6
>=3B >=3B users.
= >=3B >=3B >=3B Thank you very much for your precious advice.
>= =3B >=3B >=3B Best regards
>=3B >=3B >=3B Sherin AlfalahTo
= >=3B >=3B >=3B recover the email address of the author of the message= =2C please change
>=3B >=3B >=3B the strange characters on the top= line to the -$- sign. You can also
>=3B >=3B >=3B look up the
= >=3B >=3B X-
>=3B >=3B >=3B Original-From: line in the mail he= ader.To
>=3B >=3B recover the email address of the author of the mes= sage=2C please change the
>=3B >=3B strange characters on the top li= ne to the (-) sign. You can also look up the
>=3B X-
>=3B >=3B = Original-From: line in the mail header.
>=3B
>=3B
>=3B -= =3D This is automatically added to each message by the mailing script =3D-<= br>>=3B To recover the email address of the author of the message=2C plea= se change
>=3B the strange characters on the top line to the ~~ sign. Y= ou can also
>=3B=
>=3B
>=3B
&= gt=3B
>=3B
&= gt=3B
>=3B =
>=3B
>=3B =
>=3B http://www.ccl.net/chemistry/sub_un= sub.shtml
>=3B
>=3B Before posting=2C check wait time at: http:/= /www.ccl.net
>=3B
>=3B
>=3B C= onferences: http://server.ccl.net/chemistry/announcements/conferences/
&= gt=3B
>=3B Search Messages: http://www.ccl.net/chemistry/searchccl/in= dex.shtml
>=3B
>=3B If your mail bounces from CCL with 5.7.1 err= or=2C check:
>=3B
>=3B
= >=3B
>=3B =
>=3B
= --_3b4a401a-8acf-45ca-b458-0a7398150ef0_-- From owner-chemistry@ccl.net Mon May 27 10:52:00 2013 From: "kalyan onekalyan##yahoo.com" To: CCL Subject: CCL:G: How to characterize and change the tacticity of polymer chain Message-Id: <-48737-130527070912-2256-tDeFkKeKAMIk72IQXPQkog ~ server.ccl.net> X-Original-From: kalyan Content-Type: multipart/alternative; boundary="2164780-1194681031-1369652944=:53736" Date: Mon, 27 May 2013 04:09:04 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: kalyan [onekalyan:_:yahoo.com] --2164780-1194681031-1369652944=:53736 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable =A0Hi=A0=0A=A0Chaofu Wu=0A=A0=A0=0A=A0Just use Z-matrix (Molden Visualizati= on programme ) ( Molden also Default program for G03 or Gaussian )=0A=0A=A0= you can also use =A0accelrys Discovery Studio Overview=0A=0A=0Awith my kind= regards=0Akalyan=A0=0A____________________________________________________= ______________=0AKalyan Kumar Dhar (MS,PhD)=A0=0APolitecnico di Milano=A0= =0AT: +39.02.2399.4742/3107/3106=0AM: +39.388.753.0822=0AE: kdhar() chem.po= limi.it=A0=0AF :+39.02.2399.3180/3080=0A___________________________________= __________________________________=0AFacebook : http://www.facebook.com/Eng= ineer.Partha=0ALinkedIn : http://www.linkedin.com/in/onekalyan=A0=0A=0AYout= ube : http://www.youtube.com/user/onepartho=0A=0ATwitter : =A0https://twitt= er.com/onekalyan=0A=0AResearchGate: =A0https://www.researchgate.net/profile= /Kalyan_Dhar/=0A=0Ag+ : =A0 =A0 =A0 =A0 https://plus.google.com/u/0/1106332= 39418959751300/posts/p/pub=0A=0A=0A=0A=0A=0A=0A=0A=0A=0A=0A>_______________= _________________=0A> From: WuChaofu xiaowu759*o*hotmail.com =0A>To: "Dhar, Kalyan kumar " =0A>Sent: Monday, May 27, 2013 12:32 PM=0A>Subject: CCL: How to characte= rize and change the tacticity of polymer chain=0A> =0A>=0A>=0A>Sent to CCL = by: WuChaofu [xiaowu759=3D-=3Dhotmail.com]=0A>Dear CCLers,=0A>I have an ato= mistic model (pdb file), which is an isotactic=A0polymer chain. From the vi= sualized model, I can tell the tacticity. =A0However, how to characterize t= he tacticity using some geometric parameters (i.e., bond angles, dihedral a= ngles)? And how to change the tacticity from isotactic to syndiotactic by s= ome geometric operations? Thanks a lot for any reply to this letter.=0A>You= rs sincerely,=0A>Chaofu Wu=0A>=0A>=0A>=0A>-=3D This is automatically added = to each message by the mailing script =3D-=0A>To recover the email address = of the author of the message, please change=0A>the strange characters on th= e top line to the #,# sign. You can also=0A>look up the X-Original-From: line= in the mail header.=0A>=0A>E-mail to subscribers: CHEMISTRY#,#ccl.net or use= :=0A>=A0 =A0 =A0=0A>=0A>E-m= ail to administrators: CHEMISTRY-REQUEST#,#ccl.net or use=0A>=A0 =A0 =A0 http= ://www.ccl.net/cgi-bin/ccl/send_ccl_message=0A>=0A= =0A>=A0 =A0 =A0=0A>=0A>Before = posting, check wait time at: http://www.ccl.net=0A>=0A>Job: http://www.ccl.= net/jobs =0A>Conferences: http://server.ccl.net/chemistry/announcements/con= ferences/=0A>=0A>Search Messages: http://www.ccl.net/chemistry/searchccl/in= dex.shtml=0A>=0A=0A>= =A0 =A0 =A0=0A>=0A>RTFI: http://www.ccl.net= /chemistry/aboutccl/instructions/=0A>=0A>=0A>=0A>=0A>=0A>=0A> --2164780-1194681031-1369652944=:53736 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
 Hi 
=  Chaofu Wu=
 &nbs= p;
&= nbsp;Just use Z-matrix (Molden Visualization programme ) ( Molden also Default progr= am for G03 or Gaussian )
 you can also use=  accelrys Discovery Studio Overview



with my kind regards
kalyan 
______________= ____________________________________________________
Kalyan Kumar= Dhar (MS,PhD) 
Politecnico di Milano 
T: +39= .02.2399.4742/3107/3106
M: +39.388.753.0822
E: kdhar() = chem.polimi.it 
F :+39.02.2399.3180/3080
_________________________________________= ____________________________
Facebook : http://www.facebook.com/E= ngineer.Partha
LinkedIn : http://www.linkedin.com/in/onekalyan&nb= sp;
Youtube : http://www.youtube.com/user/onepartho
=
Twitter :  https://twitter.com/onekalyan
ResearchGa= te:  https://www.researchgate.net/profile/Kalyan_Dhar/
g= + :         https://plus.google.com/u/0/110633239418959= 751300/posts/p/pub







<= b>From: WuChaofu xiaowu759*o*h= otmail.com <owner-chemistry#,#ccl.net>
To: "Dhar, Kalyan kumar " <kalyan.dhar#,#mail.p= olimi.it>
Sent: Mo= nday, May 27, 2013 12:32 PM
Subje= ct: CCL: How to characterize and change the tacticity of polymer= chain

=0A
Sent to= CCL by: WuChaofu [xiaowu759=3D-=3Dhotmail.com]
Dear CCLers,
I have a= n atomistic model (pdb file), which is an isotactic polymer chain. Fro= m the visualized model, I can tell the tacticity.  However, how to cha= racterize the tacticity using some geometric parameters (i.e., bond angles,= dihedral angles)? And how to change the tacticity from isotactic to syndio= tactic by some geometric operations? Thanks a lot for any reply to this let= ter.
Yours sincerely,
Chaofu Wu



-=3D This is automatic= ally added to each message by the mailing script =3D-
To recover the ema= il address of the author of the message, please change
the strange chara= cters on the top line to the #,# sign. You can also
look up the X-Original= -From: line in the mail header.

E-mail to subscribers: CHEMISTRY#,#ccl.= net or use:
     

E-mail to administr= ators: CHEMISTRY-REQUEST#,#ccl.net or use
   =   http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subs= cribe/Unsubscribe:
      http://www.ccl.net/chemistry/su= b_unsub.shtml
Conferences: http://server.ccl.net= /chemistry/announcements/conferences/

Search Messages: http://www.cc= l.net/chemistry/searchccl/index.shtml

If your mail bounces from CCL = with 5.7.1 error, check:
      http://www.ccl.net/spammer= s.txt
<= br>




=20 --2164780-1194681031-1369652944=:53736-- From owner-chemistry@ccl.net Mon May 27 11:26:00 2013 From: "WuChaofu xiaowu759!A!hotmail.com" To: CCL Subject: CCL: How to characterize and change the tacticity of polymer chain Message-Id: <-48738-130527104146-18034-zrAaWIavz1DGymzoFj9dew[*]server.ccl.net> X-Original-From: WuChaofu Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="gb2312" Date: Mon, 27 May 2013 22:41:35 +0800 MIME-Version: 1.0 Sent to CCL by: WuChaofu [xiaowu759^-^hotmail.com] Dear Petitjean, Thanks again for your quick reply. ---------------------------------------- > From: owner-chemistry||ccl.net > To: xiaowu759||hotmail.com > Subject: CCL: How to characterize and change the tacticity of polymer chain > Date: Mon, 27 May 2013 12:58:49 +0200 > > > Sent to CCL by: Michel Petitjean [petitjean.chiral\a/gmail.com] > Dear Chaofu, > Even for one asymmetric carbon it is hard to build a program > implementing the CIP rules working in any case (in fact the CIP rules > do not work in any case), and even recognizing an asymmetric carbon > can be hard: the main difficulty is to check when two substituents are > different or not. > For a specific class of polymers, a simplified analysis to locate the > stereocenters and prioritize the substituents should be easier. > Once done, flagging the polymer as isotactic or syndiotactic or none > of them is easy, even if you use some house defined priority rules > rather than the CIP ones. > In any case, once the asymmetric carbon is recognized and once its > four substituents 1<2<3<4 are prioritized, you may perform as follows: > (1) put the carbon at the origin, (2) check if the centered trihedron Is this "carbon" in step 1 the asymmetric carbon or that in the substituent "1"? > 2->3->4 is direct or not (i.e. compute the sign of the determinant > [2,3,4]), (3) assign the desired stereo flag. > Isotactic/syndiotactic analysis reduces to check the sequence of flags. > Hope it helps. > Best, > Michel. > > Michel Petitjean > MTi, INSERM UMR-S 973, University Paris 7, > 35 rue Helene Brion, 75205 Paris Cedex 13, France. > Phone: +331 5727 8434; Fax: +331 5727 8372 > E-mail: petitjean.chiral_-_gmail.com (preferred), > michel.petitjean_-_univ-paris-diderot.fr > http://petitjeanmichel.free.fr/itoweb.petitjean.html > > > 2013/5/27 WuChaofu xiaowu759*o*hotmail.com : >> >> Sent to CCL by: WuChaofu [xiaowu759=-=hotmail.com] >> Dear CCLers, >> I have an atomistic model (pdb file), which is an isotactic polymer chain. From the visualized model, I can tell the tacticity. However, how to characterize the tacticity using some geometric parameters (i.e., bond angles, dihedral angles)? And how to change the tacticity from isotactic to syndiotactic by some geometric operations? Thanks a lot for any reply to this letter. >> Yours sincerely, >> Chaofu Wu> > From owner-chemistry@ccl.net Mon May 27 13:12:00 2013 From: "Ayyaz Mahmood ayyazcmc .. gmail.com" To: CCL Subject: CCL: Error finding transition state Message-Id: <-48739-130527113202-24130-nrUZlgP0Ja1ajWeUVJqFVA[#]server.ccl.net> X-Original-From: "Ayyaz Mahmood" Date: Mon, 27 May 2013 11:32:00 -0400 Sent to CCL by: "Ayyaz Mahmood" [ayyazcmc~~gmail.com] Hello Everyone here, I am having a problem in finding the transition state, there is one imaginary frequency but the calculations finish with link error 9999. What I saw in the optimization steps, the structure is stuck and dont move any way. I tried changing vibrational modes manually but it did not work. Pleas, anyone can help me here. Thanks and Regards Ayyaz Ayyazcmc(_)gmail.com Department of chemistry, UFPE, Brazil From owner-chemistry@ccl.net Mon May 27 13:47:00 2013 From: "Jim Kress ccl_nospam(_)kressworks.com" To: CCL Subject: CCL: Server qualities Message-Id: <-48740-130527125518-5158-+Ba3Dkx1C8WC5jJIHlha7w^server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 27 May 2013 12:55:18 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam * kressworks.com] Johannes, I thought your response was just fine. If other people felt differently that's their problem. If they have grievances against Dell (or any other computer manufacturer) they should air them in this forum as a public response, rather than attacking you personally. Their lack of willingness to voice their opinions publicly indicates, to me, a lack of intellectual honesty and personal courage or a conflict of interest they are afraid to reveal. Jim -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com()ccl.net [mailto:owner-chemistry+ccl_nospam==kressworks.com()ccl.net] On Behalf Of Johannes Hachmann jh++chemistry.harvard.edu Sent: Sunday, May 26, 2013 7:59 PM To: Kress, Jim Subject: CCL: Server qualities Sent to CCL by: "Johannes Hachmann" [jh~~chemistry.harvard.edu] Dear Sherin, I received an off-list eMail with a rather stiff blowback on my previous note which made me realize that I should have been more careful in my formulation. First, let me stress that I don't have any direct or indirect stake whatsoever (financial or otherwise) in Dell or any other hardware company, nor do I have an agenda on the topic of hardware. My eMail was not a formal endorsement or advertisement of any kind, and I did not mean to suggest that the hardware I mentioned is better than its competitors. I only wanted to share my personal experience - for whatever that's worth. If this intention was misunderstood I sincerely apologize! It was suggested that my opinion is biased and that is indeed the case because I know the R420/R620 and the similar C6100/C6220 series. I've been happy with both (although it was explained to me that the latter actually has a substandard RAID controller and I/O performance), which I cannot claim for all clusters I used. I also appreciate the responsiveness of the Dell reps in for quotes and customization requests (although my latest contact was subpar), the pricing seems fair, the professional sys admins I talk to in two academic research computing centers seem to like the Dells (although they use a wide assortment of other hardware as well). The centers I'm familiar with have thousands of cores in these systems. So, for whatever anecdotal evidence is worth, this suggestion at least does not seem farfetched. The biggest criticism I received was regarding bad business, labor, environmental, and customer practices by Dell. I personally had only positive experience with respect to the last point (both for high-performance computing and personal laptops I used to have). I really have no idea whether Dell is particularly bad with respect to labor, environment, and business practices - my impression is that all the big companies produce in the same Foxconn facility in China and are equally guilty of dubious behavior. But I may well be wrong on this. I would very much appreciate to hear of people's less positive experience with the mentioned hardware - I'm always happy to learn. For the time being I wanted to mention a system which I don't know first hand, but I like the idea and admire the scientist behind it: http://pqs-chem.com/ Maybe that's the right computer for you. Here is another resource that may be helpful in your search: http://www.siliconmechanics.com/ Best wishes and my apologies for any irritations I may have caused earlier, Johannes ----------------------------------------------- Dr. Johannes Hachmann Research Associate Harvard University Department of Chemistry and Chemical Biology 12 Oxford St, Rm M104A Cambridge, MA 02138 ----------------------------------------------- > -----Original Message----- > From: owner-chemistry+jh==chemistry.harvard.edu(-)ccl.net > [mailto:owner- > chemistry+jh==chemistry.harvard.edu(-)ccl.net] On Behalf Of Johannes > Hachmann jh|-|chemistry.harvard.edu > Sent: Sunday, 26 May, 2013 11:49 > To: Hachmann, Johannes > Subject: CCL: Server qualities > > > Sent to CCL by: "Johannes Hachmann" [jh,+,chemistry.harvard.edu] Hi Sherin, > > Such a purchase decision very much depends on what kind of studies you want > to do, but (without wanting to make undue advertisement) the Dell R420/R620 > chassis is a pretty good design and value, in particular if you > already have a > suitable rack. Then you can fit the nodes with the CPUs, RAM, IB etc according > to your needs. Again, this is just one solution which happens to work > well for quantum chemistry but there are many others. > > Best > > Johannes > > ----------------------------------------------- > Dr. Johannes Hachmann > Research Associate > Harvard University > Department of Chemistry and Chemical Biology > 12 Oxford St, Rm M104A > Cambridge, MA 02138 > ----------------------------------------------- > > > > > -----Original Message----- > > From: owner-chemistry+jh==chemistry.harvard.edu-$-ccl.net > > [mailto:owner- > > chemistry+jh==chemistry.harvard.edu-$-ccl.net] On Behalf Of Sherin > > chemistry+Alfalah > > shireen.alfalah],[yahoo.com > > Sent: Sunday, 26 May, 2013 04:47 > > To: Hachmann, Johannes > > Subject: CCL: Server qualities > > > > > > Sent to CCL by: "Sherin Alfalah" [shireen.alfalah-,-yahoo.com] > > Dear CCL users, > > I am wondering if I can have a kind advice on the qualifications of > > a > server that > > is supposed to run molecular or quantum chemistry calculations for > > systems constituted of 60-70 atoms. The server is planned to be used > > by 5 or 6 > users. > > Thank you very much for your precious advice. > > Best regards > > Sherin AlfalahTo > > recover the email address 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: line in the mail header.To > recover the email address 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: line in the mail header.http://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 Mon May 27 21:16:01 2013 From: "WuChaofu xiaowu759,,hotmail.com" To: CCL Subject: CCL: How to characterize and change the tacticity of polymer chain Message-Id: <-48741-130527211430-27382-Mq1Mdq8sq5MgWcUTJHqT/A#%#server.ccl.net> X-Original-From: WuChaofu Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="gb2312" Date: Tue, 28 May 2013 09:14:23 +0800 MIME-Version: 1.0 Sent to CCL by: WuChaofu [xiaowu759[a]hotmail.com] Dear Michel, Thank you very much! You surely give such a good suggestion. However, I can not quite understand why the tacticity of polymer chains can be determined by computing the sign of determinant [2,3,4]. Could you explain it further, please? Yours sincerely, Chaofu Wu > ---------------------------------------- >> Date: Mon, 27 May 2013 18:04:34 +0200 >> Subject: Re: CCL: How to characterize and change the tacticity of polymer chain >> From: petitjean.chiral:gmail.com >> To: xiaowu759:hotmail.com >> >> Carbon is the asymmetric carbon, assumed to have coordinates (x,y,z)=(0,0,0). >> Best regards, >> Michel. >> >> 2013/5/27 WuChaofu xiaowu759!A!hotmail.com : >>> >>> Sent to CCL by: WuChaofu [xiaowu759^-^hotmail.com] >>> Dear Petitjean, >>> Thanks again for your quick reply. >>> ---------------------------------------- >>>> From: owner-chemistry+/-ccl.net >>>> To: xiaowu759+/-hotmail.com >>>> Subject: CCL: How to characterize and change the tacticity of polymer chain >>>> Date: Mon, 27 May 2013 12:58:49 +0200 >>>> >>>> >>>> Sent to CCL by: Michel Petitjean [petitjean.chiral\a/gmail.com] >>>> Dear Chaofu, >>>> Even for one asymmetric carbon it is hard to build a program >>>> implementing the CIP rules working in any case (in fact the CIP rules >>>> do not work in any case), and even recognizing an asymmetric carbon >>>> can be hard: the main difficulty is to check when two substituents are >>>> different or not. >>>> For a specific class of polymers, a simplified analysis to locate the >>>> stereocenters and prioritize the substituents should be easier. >>>> Once done, flagging the polymer as isotactic or syndiotactic or none >>>> of them is easy, even if you use some house defined priority rules >>>> rather than the CIP ones. >>>> In any case, once the asymmetric carbon is recognized and once its >>>> four substituents 1<2<3<4 are prioritized, you may perform as follows: >>>> (1) put the carbon at the origin, (2) check if the centered trihedron >>> >>> Is this "carbon" in step 1 the asymmetric carbon or that in the substituent "1"? >>> >>>> 2->3->4 is direct or not (i.e. compute the sign of the determinant >>>> [2,3,4]), (3) assign the desired stereo flag. >>>> Isotactic/syndiotactic analysis reduces to check the sequence of flags. >>>> Hope it helps. >>>> Best, >>>> Michel. >>>> >>>> Michel Petitjean >>>> MTi, INSERM UMR-S 973, University Paris 7, >>>> 35 rue Helene Brion, 75205 Paris Cedex 13, France. >>>> Phone: +331 5727 8434; Fax: +331 5727 8372 >>>> E-mail: petitjean.chiral_-_gmail.com (preferred), >>>> michel.petitjean_-_univ-paris-diderot.fr >>>> http://petitjeanmichel.free.fr/itoweb.petitjean.html >>>> >>>> >>>> 2013/5/27 WuChaofu xiaowu759*o*hotmail.com : >>>>> >>>>> Sent to CCL by: WuChaofu [xiaowu759=-=hotmail.com] >>>>> Dear CCLers, >>>>> I have an atomistic model (pdb file), which is an isotactic polymer chain. From the visualized model, I can tell the tacticity. However, how to characterize the tacticity using some geometric parameters (i.e., bond angles, dihedral angles)? And how to change the tacticity from isotactic to syndiotactic by some geometric operations? Thanks a lot for any reply to this letter. >>>>> Yours sincerely, >>>>> Chaofu Wu>>> >>>