From owner-chemistry@ccl.net Fri May 6 02:03:00 2011 From: "ABHISHEK SHAHI shahi.abhishek1984^-^gmail.com" To: CCL Subject: CCL:G: converged and minima Message-Id: <-44564-110506015544-8459-TlvjoS31L143hi97Y8/JiA##server.ccl.net> X-Original-From: ABHISHEK SHAHI Content-Type: multipart/alternative; boundary=0016e644c6c897192404a295232e Date: Fri, 6 May 2011 11:25:37 +0530 MIME-Version: 1.0 Sent to CCL by: ABHISHEK SHAHI [shahi.abhishek1984*_*gmail.com] --0016e644c6c897192404a295232e Content-Type: text/plain; charset=ISO-8859-1 Dear All, My gaussian output showing: geometry converged at one structure(i. e. four times YES) and minimum energy at another structure(slightly different from first one). Ideally these both should be same. which energy should i take for my analysis ?? 1. Energy corresponds to minima. OR 2. Energy corresponds to converged structure Thanking a lot. ######################################################## With regards; *ABHISHEK SHAHI* *Research Scholar Inorganic and Physical Chemistry Indian Institute Of Science Bangalore-12* --0016e644c6c897192404a295232e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All,

=A0 My gaussian output showing: geometry converged at one= structure(i. e. four times YES) and minimum energy at another structure(sl= ightly different from first one). Ideally these both should be same. which = energy should i take for my analysis ??
1. Energy corresponds to minima. OR
2. Energy corresponds to converged s= tructure


Thanking a lot.




#############################= ###########################

With regards;
=A0<= span style=3D"color:rgb(51, 51, 255)">ABHISHEK SHAHI


Research ScholarInorganic= and Physical Chemistry
In= dian Institute Of Science
Bangalore-12


--0016e644c6c897192404a295232e-- From owner-chemistry@ccl.net Fri May 6 08:20:00 2011 From: "psavita~!~crlindia.com" To: CCL Subject: CCL: molecular modelling software Message-Id: <-44565-110506005129-2418-gMJ4SwB2nBbgmQXD9fisEQ^_^server.ccl.net> X-Original-From: psavita-#-crlindia.com Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Date: Fri, 6 May 2011 10:26:43 +0530 MIME-Version: 1.0 MIME-Version: 1.0 Sent to CCL by: psavita[*]crlindia.com
Hello Frank,

My experience with Materials Studio from Ac= celrys has been very good.
The front-end GUI makes things quite simple p= lus a variety of tools
from ab initio to MD are supported.
The prici= ng is a bit too high though.

Thanks and best wishes,

Savita Pundlik
Computational Materials Ap= plied Research Group
Computational Research Laboratories= Ltd.,
Taco House, Damle Path, Off Law Co= llege Road
Pune - 411= 004, India.



-----owner-chemistry+psavita=3D=3Dcrlindia.com]=[ccl.net= wrote: -----

To: "Pundlik, Savita Sunil " <psavita]=[crlindia.com><= br>From: "Frank von Horsten frank.von-horsten[a]atotech.com" <owner-chem= istry]=[ccl.net>
Sent by: owner-chemis= try+psavita=3D=3Dcrlindia.com]=[ccl.net
Date: 05/05/2011 02:26PM
Su= bject: CCL: molecular modelling software


Sent to CCL by: "Frank  von Horsten" = [frank.von-horsten++atotech.com]
Dear all,

We are interested in a= n integrated molecular modelling program suit for commercial use, which cou= ld be used in areas such as adhesion promotion, organic electronics and cor= rosion protection.

Currently, we are looking into Accelrys (Material= s Studio), Materials Design, Scienomics and CULGI. Does anyone have any exp= erience with one (or more) of these programs? We would be interested in adv= antages and disadvantages regarding the above mentioned topics. Do you have= any rough idea about the pricing for commercial purposes of these programs= ?

Also, suggestions of other alternatives would be highly appreciate= d.

Thanks in advance,

Frank von Horsten



-=3D T= his is automatically added to each message by the mailing script =3D-
To= recover the email address of the author of the message, please change
t= he strange characters on the top line to the ]=[ sign. You can also
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= From owner-chemistry@ccl.net Fri May 6 08:55:00 2011 From: "Tom Hawkins tom.hawkins[-]innospecinc.com" To: CCL Subject: CCL: molecular modelling software Message-Id: <-44566-110506041819-29259-hqU1GQ/Hoz+7RZoplGdmDQ ~~ server.ccl.net> X-Original-From: "Tom Hawkins" Date: Fri, 6 May 2011 04:18:16 -0400 Sent to CCL by: "Tom Hawkins" [tom.hawkins^^innospecinc.com] > "Frank von Horsten frank.von-horsten[a]atotech.com" wrote: > We are interested in an integrated molecular modelling program suit for commercial use, which could be used in areas such as adhesion promotion, organic electronics and corrosion protection. How many users of the software will there be, and what level of expertise will they have? Tom From owner-chemistry@ccl.net Fri May 6 09:30:00 2011 From: "Close, David M. CLOSED:mail.etsu.edu" To: CCL Subject: CCL:G: converged and minima Message-Id: <-44567-110506081952-15756-6gpIHVizq3OVeiXPdN9D2Q(!)server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_9D6140C35ABD534F9C463F41FC3A9CC141FA045Betsums2etsuedu_" Date: Fri, 6 May 2011 12:19:37 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED_._mail.etsu.edu] --_000_9D6140C35ABD534F9C463F41FC3A9CC141FA045Betsums2etsuedu_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Abhishek: There is not enough information to determine just what is the problem her= e. But one possibility is that the convergence is to a transition state. = This is easy to determine with a frequency calculation. A transition state= will have 1 imaginary frequency (a negative eigenvalue). If so, a displac= ement of the coordinates along the direction indicated by the negative eige= nvector should lead to a lower energy stationary point after re-optimizing. Regards, Dave Close. > From: owner-chemistry+closed=3D=3Detsu.edu-#-ccl.net [mailto:owner-chemistry+= closed=3D=3Detsu.edu-#-ccl.net] On Behalf Of ABHISHEK SHAHI shahi.abhishek198= 4^-^gmail.com Sent: Friday, May 06, 2011 1:56 AM To: Close, David M. Subject: CCL:G: converged and minima Dear All, My gaussian output showing: geometry converged at one structure(i. e. fou= r times YES) and minimum energy at another structure(slightly different fro= m first one). Ideally these both should be same. which energy should i take= for my analysis ?? 1. Energy corresponds to minima. OR 2. Energy corresponds to converged structure Thanking a lot. ######################################################## With regards; ABHISHEK SHAHI Research Scholar Inorganic and Physical Chemistry Indian Institute Of Science Bangalore-12 --_000_9D6140C35ABD534F9C463F41FC3A9CC141FA045Betsums2etsuedu_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Abhishek:=

  There is not enoug= h information to determine just what is the problem here.  But one pos= sibility is that the convergence is to a transition state.  This is ea= sy to determine with a frequency calculation.  A transition state will= have 1 imaginary frequency (a negative eigenvalue).  If so, a displac= ement of the coordinates along the direction indicated by the negative eige= nvector should lead to a lower energy stationary point after re-optimizing.=

  Regards, Dave Clos= e.

 

From: owner-chemistry+closed=3D=3Detsu.edu= -#-ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu-#-ccl.net] On Behalf= Of ABHISHEK SHAHI shahi.abhishek1984^-^gmail.com
Sent: Frida= y, May 06, 2011 1:56 AM
To: Close, David M.
Subject: CC= L:G: converged and minima

<= o:p> 

Dea= r All,

  My gaussian output showing: geometry converged at one= structure(i. e. four times YES) and minimum energy at another structure(sl= ightly different from first one). Ideally these both should be same. which = energy should i take for my analysis ??
1. Energy corresponds to minima.= OR
2. Energy corresponds to converged structure


Thanking a = lot.




######################################= ##################

With regards;
 ABHISHEK SHAHI
=
Research Scholar
Inorganic and Physical= Chemistry
Indian Institute Of S= cience
Bangalore-12

= --_000_9D6140C35ABD534F9C463F41FC3A9CC141FA045Betsums2etsuedu_-- From owner-chemistry@ccl.net Fri May 6 10:04:00 2011 From: "Anurikta Bose anurikta.bose]*[gmail.com" To: CCL Subject: CCL: To begin with computational chemistry Message-Id: <-44568-110506085358-26055-/ZnvYLLabE3Am2J1OfKvaA[A]server.ccl.net> X-Original-From: Anurikta Bose Content-Type: multipart/alternative; boundary=001636d34640f4248304a29afac4 Date: Fri, 6 May 2011 14:53:45 +0200 MIME-Version: 1.0 Sent to CCL by: Anurikta Bose [anurikta.bose(~)gmail.com] --001636d34640f4248304a29afac4 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear Prof. Mannock and others, It seems that people by now are convinced with the fact that piracy is only observed and practiced in third world countries. This made me write this email just to draw your attention to the other side of the picture. It is really unfortunate that such a generalized comment (piracy in thir= d world countries, specially in India and China) is coming from a responsible person like Prof. Mannock. I don't want to make any emotional comments here rather would go for the facts obtained from my personal experiences. I had to stay in one of the western very developed countries for some time where = I have seen people downloading not only pirated softwares, also enormous amount of pirated movies/serials. What do you call watching a football matc= h online (of course via pirated streaming). Piracy is an issue of course that I should not ignore and I also don't disagree the fact that in India piracy is there..what I can not agree is that it is only prevalent in India and China or other "third world" countries (except other western "third world" countries). I can't say anything about piracy in other western countries, like USA, but from your first email I have got the idea that in Canada piracy is practiced and you do refer pirated version of the books when necessary. Regarding the reduced price of the text books, its totally justified as the price should be relative to the local market which, I suppose, depends on the production and marketing cost. Regards, AB Mauricio, I understand your viewpoint and the piracy issue. It was not my > intention to completely trivialize the issue. I stand by what I said, tha= t > for some countries, the universities do not have enough money for teachin= g > and students cannot afford text books and software. I seem to recall abou= t > 5 > years ago, there were issues with Indian and Chinese publishers reproduci= ng > textbooks for students at a tenth of the price that we pay. Yes, librarie= s > have books, but not 300 copies of each title. The same could be said for > software in some countries, although not in Canada or Argentina. Also, ma= ny > areas of science do not have a business opportunity available to them to > raise funds to buy supplies. Academics producing books and software have > that opportunity and consider it as part of their profession and protect > those rights. Yet many do not share the revenue with the academic > intitution > where they are employed. I work in a biphysics lab that does a lot of > chemical synthesis, any outside consulting that we do is supposed to be > negotiated through a local university office so that the university can g= et > its cut for providing us with space and library facilities. A book or > software should be covered by the same rules unless it did not utilize an= y > of those facilities in my opinion. If the issue really is piracy, then th= e > academic institution is better equipped to chase people and other > institutions who pirate books or software than the author of the product. > So > as you can see, I agree that theft is an issue that needs to be dealt wit= h, > but the authors are not able to follow up the issue in law, so I think th= at > it is better to have a university partner in business that can protect > those > rights. > > Finally, as a related side issue here, I would like to ask another > question. > Some scientific labs produce patentable work/products. How many of those > patents are licensed to companies to generate local jobs? Here is Canada, > many chemical and pharmaceutical companies are either small spin-offs wit= h > no cash, or satellites of multinational companies who use the technology > elsewhere. Thus, Canadian patents may generate money for the university a= nd > a few inventors, but not generate any local jobs. what are other peoples > experience with these situations? Dave > > On Tue, May 3, 2011 at 10:20 AM, Mauricio Federico Erben erben.:. > quimica.unlp.edu.ar wrote: > > > Dave, I have some doubts regarding the terms you present the problem, > > especially about the role of the =96assumed- third world piracy. > > > > As far as I know -for example in Argentina- the science bureau pays for > the > > access to journals from several "first world" editorials, and the cost = is > > not inexpensive, actually. Indeed, in relative terms, the access to the > > information is a quite elevate amount of our modest science budgets. Th= e > > same apply for the computer programs and books available in our > > universities. > > > > The property of the knowledge, including copyright and other topics, is= a > > very interesting issue to be discussed, but the =93unfortunate reality = in > the > > third world=94, -even when only science is concerning- is beyond > piracy=85 > > please don=92t trivialize the question. > > > > Best regard, > > > > Mauricio. > > > > > > > > > > > > > > > > ----- Original Message ----- > > *From:* David A Mannock dmannock,ualberta.ca > > *To:* Erben, Mauricio Federico > > *Sent:* Monday, May 02, 2011 6:28 PM > > *Subject:* CCL: To begin with computational chemistry > > > > Jim, I know. I feel guilty every time a take an egg > from a chicken or > go > > to a cut-price movie theatre. lol The unfortunate reality is that in th= e > > third world piracy of software and text books is commonplace and there = is > > little that we can do to stop it. In order to stop it and bring those > > countries into line, there have to be electronic options put in place f= or > > teaching purposes. Once qualified, many of those people will probably b= uy > a > > hard copy to put on their bookshelf if they continue in science. > Personally, > > I smile when I see someone copy a paragraph or two from one of my paper= s > > into their own "original" work. In reality, since knowledge is power, a= nd > I > > occasionally have to pay an advertizing fee to publish, I wonder if I > should > > not be getting a royalty payment everytime someone downloads or > photocopies > > my papers. Hmm! I wonder if I could afford a Lamborghini just like my > > brothers after all? Dave > > > > On Mon, May 2, 2011 at 11:48 AM, Jim Kress ccl_nospam++kressworks.com < > > owner-chemistry:ccl.net> wrote: > > > >> There is no justification for theft. > >> > >> > >> > >> Jim Kress > >> > >> > >> > >> > From: owner-chemistry+ccl_nospam=3D=3Dkressworks.com]_[ccl.net > >> [mailto:owner-chemistry+ccl_nospam=3D=3Dkressworks.com]_[ccl.net] On B= ehalf > >> Of > >> David A Mannock dmannock(-)ualberta.ca > >> Sent: Saturday, April 30, 2011 5:13 PM > >> To: Kress, Jim > >> Subject: CCL: To begin with computational chemistry > >> > >> > >> > >> Chris, as a newbie to computational chemistry, I try to use every > resource > >> that I can get hold of. I have to admit that I sometimes pirate > electronic > >> copies to help me search texts which are often long and complicated. A > >> recent point relevant to this issue is Jacob Israelachvili's > >> "Intermolecular > >> and surface forces", 2nd Edn. As our lab copy disappeared into a black > >> hole > >> known as my colleagues basement, I found a pirated online copy of this > >> essential text. I later bought a second-hand hard copy, while awaiting > the > >> appearance of the 3rd Edition, which was due to appear in 2010, but ca= me > >> out > >> in 2011. I have read the 1991 2nd edition cover to cover and have > returned > >> to it in order to refresh my memory many times. After talking to Jacob > >> Israelachvili, he explained the delays in getting the 3rd edition to > press > >> and told me when it would be available. Within a week of it coming off > the > >> presses, I had bought a copy from Amazon out of my own pocket. The new > >> edition is several hundred pages longer than the previous copy and an > >> electronic version would be useful to me. It is a beautifully written > >> masterpiece in my opinion. However, many publishers are slow in their > move > >> into the electronic realm. This is where the future lies. > >> > >> My job ends here on June 30th, 2011, but I still have responsibilities > for > >> writing up papers for a student. I will not have access to online > library > >> facilities here because of local University policy. Despite this, I > would > >> still be willing to buy a new edition of your book to help with my > >> calculations on my Linux box. I would do this out of my own pocket if > need > >> be. > >> > >> As I see it, one of the main purposes of text books is to put all of t= he > >> knowledge in a certain area in one place for ease of reference. I thin= k > >> that > >> this is very valuable for those of us who do research and those who > teach. > >> Putting together a new edition of your book would be recognized as a > >> valuable contribution by people in this scientific area, but rather th= an > >> be > >> pessimistic about piracy, ask your publishers to make an electronic co= py > >> available for sale at 50% of the price of the softcover. A university > >> could > >> either buy a yearly site license for distribution to students at a low= er > >> price, or the institution could host a copy which could be read online= , > >> but > >> not downloaded. There will always be people who want to get something > for > >> nothing and who are willing to remove the encryption on electronic > media, > >> the simplest solution is to make the text available at a lower cost fo= r > >> academic use and make some money rather than none. You should be talki= ng > >> to > >> your publisher about this policy, as it will help their bottom line an= d > >> your > >> standard of living in your retirement!! So cheer up and realize that o= ld > >> dogs, like myself, would rather sit on a sun lounger on my back porch > >> reading your new edition, than sitting at a computer screen in the lab > or > >> in > >> my study! David Mannock > >> > >> On Sat, Apr 30, 2011 at 12:46 PM, Christopher Cramer cramer+/-umn.edu > >> wrote: > >> > >> > >> Sent to CCL by: Christopher Cramer [cramer-$-umn.edu] > >> My... > >> > >> The least you can do if you're going to steal the book, and post it > online > >> for piracy, is choose a later printing -- then people won't have to > refer > >> to > >> so many errata. > >> > >> Now I recall why I've been reluctant to devote the time to a 3rd > >> edition... > >> > >> CJC > >> > >> --001636d34640f4248304a29afac4 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable
Dear Prof. Mannock and others,

=A0=A0= It seems that people by now are convinced with the fact that piracy is on= ly observed and practiced in third world countries. This made me write this= email just to draw your attention to the other side of the picture.
=A0
=A0=A0 It is really unfortunate that such a generalized comment (pir= acy in third world countries, specially in India and China) is coming from = a responsible person like Prof. Mannock. I don't want to make any emoti= onal comments here rather would go for the facts obtained from my personal = experiences. I had to stay in one of the western very developed countries f= or some time where I have seen people downloading not only pirated software= s, also enormous amount of pirated movies/serials. What do you call watchin= g a football match online (of course via pirated streaming). Piracy is an i= ssue of course that I should not ignore and I also don't disagree the f= act that in India piracy is there..what I can not agree is that it is only = prevalent in India and China or other "third world" countries (ex= cept other western "third world" countries).=A0

=A0 I can't say anything about piracy in other western countries, l= ike USA, but from your first email I have got the idea that in Canada pirac= y is practiced and you do refer pirated version of the books when necessary= .

=A0 Regarding the reduced price of the text books, its totally justifie= d as the price should be relative to the local market which, I suppose, dep= ends on the production and marketing cost. =A0 =A0


=A0Regards,<= br> =A0AB





Mauricio, I understand your viewpoint and the piracy issue. It was not my <= br> intention to completely trivialize the issue. I stand by what I said, that<= br> for some countries, the universities do not have enough money for teaching<= br> and students cannot afford text books and software. I seem to recall about<= br> 5
years ago, there were issues with Indian and Chinese publishers reproducing=
textbooks for students at a tenth of the price that we pay. Yes, libraries<= br> have books, but not 300 copies of each title. The same could be said for software in some countries, although not in Canada or Argentina. Also, many=
areas of science do not have a business opportunity available to them to raise funds to buy supplies. Academics producing books and software have that opportunity and consider it as part of their profession and protect those rights. Yet many do not share the revenue with the academic
intitution
where they are employed. I work in a biphysics lab that does a lot of
chemical synthesis, any outside consulting that we do is supposed to be
negotiated through a local university office so that the university can get=
its cut for providing us with space and library facilities. A book or
software should be covered by the same rules unless it did not utilize any<= br> of those facilities in my opinion. If the issue really is piracy, then the<= br> academic institution is better equipped to chase people and other
institutions who pirate books or software than the author of the product. So
as you can see, I agree that theft is an issue that needs to be dealt with,=
but the authors are not able to follow up the issue in law, so I think that=
it is better to have a university partner in business that can protect
those
rights.

Finally, as a related side issue here, I would like to ask another
question.
Some scientific labs produce patentable work/products. How many of those patents are licensed to companies to generate local jobs? Here is Canada, many chemical and pharmaceutical companies are either small spin-offs with<= br> no cash, or satellites of multinational companies who use the technology elsewhere. Thus, Canadian patents may generate money for the university and=
a few inventors, but not generate any local jobs. what are other peoples experience with these situations? Dave

On Tue, May 3, 2011 at 10:20 AM, Mauricio Federico Erben erben.:.
quimica.unlp.edu.a= r <owner-chemistry-*-cc= l.net> wrote:

> =A0Dave, I have some doubts regarding the terms you present the proble= m,
> especially about the role of the =96assumed- third world piracy.
>
> As far as I know -for example in Argentina- the science bureau pays fo= r
the
> access to journals from several "first world" editorials, an= d the cost is
> not inexpensive, actually. Indeed, in relative terms, the access to th= e
> information is a quite elevate amount of our modest science budgets. T= he
> same apply for the computer programs and books available in our
> universities.
>
> The property of the knowledge, including copyright and other topics, i= s a
> very interesting issue to be discussed, but the =93unfortunate reality= in
the
> third world=94, -even when only science is concerning- is beyond
piracy=85
> please don=92t trivialize the question.
>
> Best regard,
>
> Mauricio.
>
>
>
>
>
>
>
> ----- Original Message -----
> *From:* David A Mannock dmannock,ualberta.ca <owner-chemistry],[ccl.net>
> *To:* Erben, Mauricio Federico <erben],[quimica.unlp.edu.ar>
> *Sent:* Monday, May 02, 2011 6:28 PM
> *Subject:* CCL: To begin with computational chemistry
>
> Jim, I know. I feel guilty every time a take an egg > from a chicke= n or
go
> to a cut-price movie theatre. lol The unfortunate reality is that in t= he
> third world piracy of software and text books is commonplace and there= is
> little that we can do to stop it. In order to stop it and bring those<= br> > countries into line, there have to be electronic options put in place = for
> teaching purposes. Once qualified, many of those people will probably = buy
a
> hard copy to put on their bookshelf if they continue in science.
Personally,
> I smile when I see someone copy a paragraph or two from one of my pape= rs
> into their own "original" work. In reality, since knowledge = is power, and
I
> occasionally have to pay an advertizing fee to publish, I wonder if I<= br> should
> not be getting a royalty payment everytime someone downloads or
photocopies
> my papers. Hmm! I wonder if I could afford a Lamborghini just like my<= br> > brothers after all? Dave
>
> On Mon, May 2, 2011 at 11:48 AM, Jim Kress ccl_nospam++kressworks.com <
> owner-chemistry:ccl.net> wrote:
>
>> There is no justification for theft.
>>
>>
>>
>> Jim Kress
>>
>>
>>
>> > From: owner-chemistry+ccl_nospam=3D=3D
kressworks.com]_[ccl.net
>> [mailto:owner-chemistry+ccl_nospam=3D=3Dkressworks.com]_[ccl.net] On Behalf
>> Of
>> David A Mannock dmannock(-)ualberta.ca
>> Sent: Saturday, April 30, 2011 5:13 PM
>> To: Kress, Jim
>> Subject: CCL: To begin with computational chemistry
>>
>>
>>
>> Chris, as a newbie to computational chemistry, I try to use every<= br> resource
>> that I can get hold of. I have to admit that I sometimes pirate electronic
>> copies to help me search texts which are often long and complicate= d. A
>> recent point relevant to this issue is Jacob Israelachvili's >> "Intermolecular
>> and surface forces", 2nd Edn. As our lab copy disappeared int= o a black
>> hole
>> known as my colleagues basement, I found a pirated online copy of = this
>> essential text. I later bought a second-hand hard copy, while awai= ting
the
>> appearance of the 3rd Edition, which was due to appear in 2010, bu= t came
>> out
>> in 2011. I have read the 1991 2nd edition cover to cover and have<= br> returned
>> to it in order to refresh my memory many times. After talking to J= acob
>> Israelachvili, he explained the delays in getting the 3rd edition = to
press
>> and told me when it would be available. Within a week of it coming= off
the
>> presses, I had bought a copy from Amazon out of my own pocket. The= new
>> edition is several hundred pages longer than the previous copy and= an
>> electronic version would be useful to me. It is a beautifully writ= ten
>> masterpiece in my opinion. However, many publishers are slow in th= eir
move
>> into the electronic realm. This is where the future lies.
>>
>> My job ends here on June 30th, 2011, but I still have responsibili= ties
for
>> writing up papers for a student. I will not have access to online<= br> library
>> facilities here because of local University policy. Despite this, = I
would
>> still be willing to buy a new edition of your book to help with my=
>> calculations on my Linux box. I would do this out of my own pocket= if
need
>> be.
>>
>> As I see it, one of the main purposes of text books is to put all = of the
>> knowledge in a certain area in one place for ease of reference. I = think
>> that
>> this is very valuable for those of us who do research and those wh= o
teach.
>> Putting together a new edition of your book would be recognized as= a
>> valuable contribution by people in this scientific area, but rathe= r than
>> be
>> pessimistic about piracy, ask your publishers to make an electroni= c copy
>> available for sale at 50% of the price of the softcover. A univers= ity
>> could
>> either buy a yearly site license for distribution to students at a= lower
>> price, or the institution could host a copy which could be read on= line,
>> but
>> not downloaded. There will always be people who want to get someth= ing
for
>> nothing and who are willing to remove the encryption on electronic=
media,
>> the simplest solution is to make the text available at a lower cos= t for
>> academic use and make some money rather than none. You should be t= alking
>> to
>> your publisher about this policy, as it will help their bottom lin= e and
>> your
>> standard of living in your retirement!! So cheer up and realize th= at old
>> dogs, like myself, would rather sit on a sun lounger on my back po= rch
>> reading your new edition, than sitting at a computer screen in the= lab
or
>> in
>> my study! David Mannock
>>
>> On Sat, Apr 30, 2011 at 12:46 PM, Christopher Cramer cramer+/-umn.edu
>> <owner-chemistry++= ccl.net> wrote:
>>
>>
>> Sent to CCL by: Christopher Cramer [cramer-$-umn.edu]
>> My...
>>
>> The least you can do if you're going to steal the book, and po= st it
online
>> for piracy, is choose a later printing -- then people won't ha= ve to
refer
>> to
>> so many errata.
>>
>> Now I recall why I've been reluctant to devote the time to a 3= rd
>> edition...
>>
>> CJC
>>
>>


--001636d34640f4248304a29afac4-- From owner-chemistry@ccl.net Fri May 6 18:18:01 2011 From: "David A Mannock dmannock]*[ualberta.ca" To: CCL Subject: CCL: To begin with computational chemistry Message-Id: <-44569-110506171253-12750-/dTV3o2+EyubDzykNYkCzw() server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=bcaec51a7d5a7679cd04a2a1f3b8 Date: Fri, 6 May 2011 15:12:44 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock#,#ualberta.ca] --bcaec51a7d5a7679cd04a2a1f3b8 Content-Type: text/plain; charset=ISO-8859-1 Anurikta, Put your moral indignation aside for the moment. Yes, piracy happens everywhere, but we are not talking about soccer games here, but text books and software. Many of the major computer chemistry software programs come from Western companies and texts relevant to that software generally cost more money than is available to a student in a third world country. If I borrow something from the internet as a trial or an illegal copy, I try out the software or book and if it is useful, I go ahead with a personal purchase (Yes, out of my own pocket!!) or get something through my institution. Incidentally, I have purchased lower priced texts of interest to me from publishers in India and they are similar in price to the Dover classics available on Amazon. The difference in price is an order of magnitude. My focus on China and India is simply that there have been many news items here over the past 10 years about exactly this type of piracy and the reluctance of the respective institutions and governments to take positive steps to eliminate it. What I am saying is that I understand the need for students in non-western countries to get what they need to have an education. Research and higher education is expensive and even in countries like Canada, money for such things is very tight. Part of the piracy problem is that some publishing houses are trying to cut costs by outsourcing the printing of the books, presumably through the transfer of electronic media to those countries. One of the arguments that I have made here is for proper assertion of the rights of authorship through the universities commercial offices and publishing houses to stamp out institutional piracy. It was pointed out on this forum that the web site on which Prof Cramer's book was stored was at an Indian institution. I suspect that a blind eye is turned to such practices by both the institution and the local government. Here it is feasible for the publishing or software company or the author to make the accusation of plagiarism or piracy in the civil court and sue. This is not easily done in other countries and the amount of any settlement may itself be dictated by the local market rather than the market where the product was developed. If you feel strongly that this practice should be stamped out in your own institution, try approaching your VP research and see if you can accomplish this. My guess is that you will receive nothing more than lip-service from the senior administration and that no one will want to touch this issue with a barge pole. Here on my lab computers, I am not permitted to install illegal copies of software and as a general rule, I do not download textbooks that I do not consider for purchase. When my responsibilities for writing up manuscripts ends here and I have to find a job elsewhere, all university licensed software will need to be uninstalled from my lab and home computers. In fact, I was reminded of this by our IT support person this week. Today, everyone wants their buck. There is no escaping this. Dave --bcaec51a7d5a7679cd04a2a1f3b8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Anurikta, Put your moral indignation aside for the moment. Yes, piracy happ= ens everywhere, but we are not talking about soccer games here, but text bo= oks and software. Many of the major computer chemistry software programs co= me from Western companies and texts relevant to that software generally cos= t more money than is available to a student in a third world country. If I = borrow something from the internet as a trial or an illegal copy, I try out= the software or book and if it is useful, I go ahead with a personal purch= ase (Yes, out of my own pocket!!) or get something through my institution. = Incidentally, I have purchased lower priced texts of interest to me from pu= blishers in India and they are similar in price to the Dover classics avail= able on Amazon. The difference in price is an order of magnitude. My focus = on China and India is simply that there have been many news items here over= the past 10 years about exactly this type of piracy and the reluctance of = the respective institutions and governments to take positive steps to elimi= nate it. What I am saying is that I understand the need for students in non= -western countries to get what they need to have an education. Research and= higher education is expensive and even in countries like Canada, money for= such things is very tight.

Part of the piracy problem is that some publishing houses are trying to= cut costs by outsourcing the printing of the books, presumably through the= transfer of electronic media to those countries. One of the arguments that= I have made here is for proper assertion of the rights of authorship throu= gh the universities commercial offices and publishing houses to stamp out i= nstitutional piracy. It was pointed out on this forum that the web site on = which Prof Cramer's book was stored was at an Indian institution. I sus= pect that a blind eye is turned to such practices by both the institution a= nd the local government. Here it is feasible for the publishing or software= company or the author to make the accusation of plagiarism or piracy in th= e civil court and sue. This is not easily done in other countries and the a= mount of any settlement may itself be dictated by the local market rather t= han the market where the product was developed. If you feel strongly that t= his practice should be stamped out in your own institution, try approaching= your VP research and see if you can accomplish this. My guess is that you = will receive nothing more than lip-service from the senior administration a= nd that no one will want to touch this issue with a barge pole.

Here on my lab computers, I am not permitted to install illegal copies = of software and as a general rule, I do not download textbooks that I do no= t consider for purchase. When my responsibilities for writing up manuscript= s ends here and I have to find a job elsewhere, all university licensed sof= tware will need to be uninstalled from my lab and home computers. In fact, = I was reminded of this by our IT support person this week. Today, everyone = wants their buck. There is no escaping this. Dave


--bcaec51a7d5a7679cd04a2a1f3b8-- From owner-chemistry@ccl.net Fri May 6 20:56:00 2011 From: "Andrew Orry andy:_:molsoft.com" To: CCL Subject: CCL: iPhone & iPad 3D Molecule Browser - iMolview Message-Id: <-44570-110506201632-3332-K6On1L9veuAbMNKbMh3bNw() server.ccl.net> X-Original-From: Andrew Orry Content-Type: multipart/alternative; boundary="------------090100000301020301070508" Date: Fri, 06 May 2011 17:13:15 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy|*|molsoft.com] This is a multi-part message in MIME format. --------------090100000301020301070508 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear All, MolSoft is excited to announce the release of an iPhone and iPad app that lets you browse protein, DNA, and drug molecules in 3D. The app has a direct link to the Protein Data Bank (PDB) and DrugBank and has a fast and easy to use interface. Touching the molecules via the screen allows you to interact immediately with the 3D structures in a unique way. You can zoom in and out, rotate, spin, pan, and clip the 3D molecules with your finger tips in ways that are impossible using a traditional mouse and desktop computer. For more details and screenshots see: http://www.molsoft.com/iMolview.html The key features are: * Easy to use touch interface. * A direct link to the Protein Data Bank (PDB) and DrugBank. * Each molecular view can be customized with a rich set of molecular representations including: wires, balls-and-sticks, space filling, ribbon diagrams, and molecular surfaces. * Zoom in and out, rotate, spin, pan, and clip the 3D molecule. * A wide selection of coloring schemes is available. * Color background, color molecule by atom type, chain, N- to C- terminal, and secondary structure. * Select residues, atoms, or chains and color or change their representations individually. * Select residues in sequence and get the corresponding selection in 3D. * Select the whole chain by holding the corresponding tab. * Display fog effect. * Set 'inertia' to the maximum and let your molecule spin in 3D indefinitely. * Display residue and site labels for the whole object or selection. * Direct link to PubMed. * Read in your own MolSoft ICM *.icb files. We hope you enjoy using the app and find it useful for your research and teaching. We welcome any feedback you may have. 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 --------------090100000301020301070508 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear All,

MolSoft is excited to announce the release of an iPhone and iPad app that lets you browse protein, DNA, and drug molecules in 3D. The app has a direct link to the Protein Data Bank (PDB) and DrugBank and has a fast and easy to use interface. Touching the molecules via the screen allows you to interact immediately with the 3D structures in a unique way. You can zoom in and out, rotate, spin, pan, and clip the 3D molecules with your finger tips in ways that are impossible using a traditional mouse and desktop computer.

For more details and screenshots see: http://www.molsoft.com/iMolview.html

The key features are:
  • Easy to use touch interface.
  • A direct link to the Protein Data Bank (PDB) and DrugBank.
  • Each molecular view can be customized with a rich set of molecular representations including: wires, balls-and-sticks, space filling, ribbon diagrams, and molecular surfaces.
  • Zoom in and out, rotate, spin, pan, and clip the 3D molecule.
  • A wide selection of coloring schemes is available.
  • Color background, color molecule by atom type, chain, N- to C- terminal, and secondary structure.
  • Select residues, atoms, or chains and color or change their representations individually.
  • Select residues in sequence and get the corresponding selection in 3D.
  • Select the whole chain by holding the corresponding tab.
  • Display fog effect.
  • Set 'inertia' to the maximum and let your molecule spin in 3D indefinitely.
  • Display residue and site labels for the whole object or selection.
  • Direct link to PubMed.
  • Read in your own MolSoft ICM *.icb files.
We hope you enjoy using the app and find it useful for your research and teaching. We welcome any feedback you may have.

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
--------------090100000301020301070508-- From owner-chemistry@ccl.net Fri May 6 22:35:00 2011 From: "Jun Zhang coolrainbow()yahoo.cn" To: CCL Subject: CCL: Program language in Quantum Chemistry: C++ or FORTRAN? Message-Id: <-44571-110506223406-31630-K8wgSODFPx0usDUPH/zwoQ++server.ccl.net> X-Original-From: Jun Zhang Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Sat, 7 May 2011 10:33:53 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: Jun Zhang [coolrainbow]*[yahoo.cn] Hello Everyone: Many new developed quantum chemistry software have been written in C++ rather than FORTRAN. Although the compilers for C++ are developing, however, due to C++'s inherent complexity, I don't think it is easier to optimize a C++ code than FORTRAN code for compilers. So why so many have chosen C++? Is it due to developing efficiency? Any suggestions will be appreciated. Jun Zhang Nankai University coolrainbow=yahoo.cn