From owner-chemistry@ccl.net Mon Oct 9 04:26:01 2006 From: "Sue Lam chsue2004,yahoo.com" To: CCL Subject: CCL: Software for Distance Measurement Between Molecules Message-Id: <-32741-061009032859-20218-3nxMRvy5RvXRLLTozuUlxg%x%server.ccl.net> X-Original-From: Sue Lam Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1632854562-1160378935=:40737" Date: Mon, 9 Oct 2006 00:28:55 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sue Lam [chsue2004]*[yahoo.com] --0-1632854562-1160378935=:40737 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear all, Thank you very much for your suggestion. Sue "Michel Petitjean ptitjean|a|itodys.jussieu.fr" wrote: Sent to CCL by: Michel Petitjean [ptitjean[]itodys.jussieu.fr] To: chemistry#%#ccl.net Subject: CCL: Re: Software for Distance Measurement Between Molecules I guess that calculating a distance between two points is not the problem. Rather, what is "the center" of a molecule: how do you define it ? Assuming n atoms, positions x1, ..., xn, some definitions are: - The mean of the atomic positions, i.e. (x1+..+xn)/n - The mass center: (M1*x1+...+Mn*xn)/(M1+...Mn) - The center of the minimal sphere containing the n atomic centers - The mean of the k vertices of the convex hull of the n atomic centers - Etc... Some of these calculations are performed by the freeware RADI: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#RADI Michel Petitjean, Email: petitjean#%#itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean#%#ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html Sent to CCL by: "Sue L" [chsue2004##yahoo.com] > Hi CCL users, > > Does anyone know any free software which can measure the distance between the center of two moleucles? > > Thanks, > Suehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1˘/min. --0-1632854562-1160378935=:40737 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear all,
 
Thank you very much for your suggestion.
 
Sue
 


"Michel Petitjean ptitjean|a|itodys.jussieu.fr" <owner-chemistry^^ccl.net> wrote:
Sent to CCL by: Michel Petitjean [ptitjean[]itodys.jussieu.fr]
To: chemistry#%#ccl.net
Subject: CCL: Re: Software for Distance Measurement Between Molecules

I guess that calculating a distance between two points is not the problem.
Rather, what is "the center" of a molecule: how do you define it ?
Assuming n atoms, positions x1, ..., xn, some definitions are:
- The mean of the atomic positions, i.e. (x1+..+xn)/n
- The mass center: (M1*x1+...+Mn*xn)/(M1+...Mn)
- The center of the minimal sphere containing the n atomic centers
- The mean of the k vertices of the convex hull of the n atomic centers
- Etc...

Some of these calculations are performed by the freeware RADI:
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#RADI

Michel Petitjean, Email: petitjean#%#itodys.jussieu.fr
ITODYS (CNRS, UMR 7086) ptitjean#%#ccr.jussieu.fr
1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57
75005 Paris, France. FAX : +33 (0)1 44 27 68 14
http://petitjeanmichel.free.fr/itoweb.petitjean.html

Sent to CCL by: "Sue L" [chsue2004##yahoo.com]
> Hi CCL users,
>
> Does anyone know any free software which can measure the distance between the center of two moleucles?
>
> Thanks,
> Sue


http://www.ccl.net/cgi-bin/ccl/send_ccl_message
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Talk is cheap. Use Yahoo! Messenger to make PC-to-Phone calls. Great rates starting at 1˘/min. --0-1632854562-1160378935=:40737-- From owner-chemistry@ccl.net Mon Oct 9 05:01:00 2006 From: "laurent favaro laurent.favaro++lpces.u-psud.fr" To: CCL Subject: CCL: Spherical Micelle Initial Guess (spatial reasoning problem) Message-Id: <-32742-061009031611-18575-ZpbS1JHcdEvvNPl4cDA1KA**server.ccl.net> X-Original-From: laurent favaro Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Mon, 09 Oct 2006 09:09:11 +0200 MIME-Version: 1.0 Sent to CCL by: laurent favaro [laurent.favaro(-)lpces.u-psud.fr] You could take fullerernes coordinates. C60 is spherical. There are two bond length, but very close. http://www.ccl.net/cca/data/fullerenes/index.shtml lf Rajan Vatassery r-vatassery,+,northwestern.edu wrote: >Sent to CCL by: "Rajan Vatassery" [r-vatassery!=!northwestern.edu] >Dear List, > I would like to provide an initial guess for a spherical micelle in order to simulate it via MD. I need to place x particles (about 100) on the surface of a sphere and they must be equally spaced from one another. Since there is no analytical solution, I've tried writing a fortran code that would come up with the initial guess from a numerical minimization. I'm currently having a lot of difficulty with the code and I am hoping that someone could send me a copy of their code (fortran,c,perl,whatever) if they've done this before. Otherwise if someone has an initial guess of about 100 particles equally spaced on the surface of a sphere (preferably in polar coordinates), I'll gladly take that as well. Thanks, > > >raj> > > > > > From owner-chemistry@ccl.net Mon Oct 9 07:13:00 2006 From: "Colette FOULIE colette.foulie!=!wanadoo.fr" To: CCL Subject: CCL: electrostatic potential Message-Id: <-32743-061009071121-27054-nXymrcMd2arbYfUROlizRg() server.ccl.net> X-Original-From: "Colette FOULIE" Date: Mon, 9 Oct 2006 07:11:20 -0400 Sent to CCL by: "Colette FOULIE" [colette.foulie!A!wanadoo.fr] Dear all, Thank you very much for your suggestion. Colette FOULIE Laboratoire de Physique, Theorie de la Matiere Condensee CNRS UMR 5027, Universite de Bourgogne. 9 avenue Alain Savary B.P 47870, F-21078 Dijon Cedex, France Tel : 03.80.39.59.50 Fax: 03.80.39.59.61 colette.foulie*_*u-bourgogne.fr From owner-chemistry@ccl.net Mon Oct 9 11:37:00 2006 From: "ReichertD(-)mir.wustl.edu" To: CCL Subject: CCL: Spherical Micelle Initial Guess (spatial reasoning problem) Message-Id: <-32744-061009112159-27714-G70m0fRkG6UJDx42vmxCbA[#]server.ccl.net> X-Original-From: ReichertD * mir.wustl.edu Content-type: multipart/related; Boundary="0__=09BBF891DFDC5C6A8f9e8a93df938690918c09BBF891DFDC5C6A" Date: Mon, 9 Oct 2006 09:36:31 -0500 MIME-Version: 1.0 Sent to CCL by: ReichertD]-[mir.wustl.edu --0__=09BBF891DFDC5C6A8f9e8a93df938690918c09BBF891DFDC5C6A Content-type: multipart/alternative; Boundary="1__=09BBF891DFDC5C6A8f9e8a93df938690918c09BBF891DFDC5C6A" --1__=09BBF891DFDC5C6A8f9e8a93df938690918c09BBF891DFDC5C6A Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: quoted-printable Hi, You might check out the program Packmol by Martinez (Mart=EDnez, J. M.;= Mart=EDnez, L. Packing optimization for automated generation of complex= system's initial configurations for molecular dynamics and docking. J. Comp. Chem. 2003, 24, 819-825.) Binaries or maybe source code can be obtained from www.ime.unicamp.br/~martinez/packmol I hope that helps. -david David Reichert, Ph.D. Asst. Professor Radiology Washington University School of Medicine 510 S. Kingshighway, Campus Box 8225 St Louis, MO 63110 e-mail: reichertd-,-wustl.edu http://scoobie.wustl.edu/ voice: (314) 362-8461 fax: (314) 362-9940 = "Rajan Vatassery = r-vatassery,+,nor = thwestern.edu" = To = Sent by: = cc owner-chemistry-,-c = cl.net Subj= ect CCL: Spherical Micelle Initial = Guess (spatial reasoning problem= ) 10/07/2006 12:18 = AM = = = Please respond to = "CCL Subscribers" = = = = Sent to CCL by: "Rajan Vatassery" [r-vatassery!=3D!northwestern.edu] Dear List, I would like to provide an initial guess for a spherical micelle in or= der to simulate it via MD. I need to place x particles (about 100) on the surface of a sphere and they must be equally spaced from one another. S= ince there is no analytical solution, I've tried writing a fortran code that= would come up with the initial guess from a numerical minimization. I'm= currently having a lot of difficulty with the code and I am hoping that= someone could send me a copy of their code (fortran,c,perl,whatever) if= they've done this before. Otherwise if someone has an initial guess of about 100 particles equally spaced on the surface of a sphere (preferab= ly in polar coordinates), I'll gladly take that as well. Thanks, raj -=3D This is automatically added to each message by the mailing script = =3D- To recover the email address of the author of the message, please chang= ehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml= Search Messages: http://www.ccl.net/htdig (login: ccl, Password: searc= h)http://www.ccl.net/spammers.txt-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-= + = --1__=09BBF891DFDC5C6A8f9e8a93df938690918c09BBF891DFDC5C6A Content-type: text/html; charset=ISO-8859-1 Content-Disposition: inline Content-transfer-encoding: quoted-printable

Hi,
You might check out the program Packmol by Martinez (Mart=EDnez, J. M.;= Mart=EDnez, L. Packing optimization for automated generation of comple= x system's initial configurations for molecular dynamics and docking. J= . Comp. Chem. 2003, 24, 819-825.) Binaries or maybe source code can be = obtained from www.ime.unicamp.br/~martinez/packmol I hope that helps. -david
David Reichert, Ph.D.
Asst. Professor Radiology
Washington University School of Medicine
510 S. Kingshighway, Campus Box 8225
St Louis, MO 63110

e-mail: reichertd-,-wustl.edu
http://scoobie.wustl.edu/
=
voice: (314) 362-8461
fax: (314) 362-9940
3D"Inactive=

          "Rajan Vatassery r-vatassery,+,northwester= n.edu" <owner-chemistry-,-ccl.net>=
          Sent by: owner-chemistry-,-ccl.net

          10/07/2006 12:18 AM =
          Please respond to
          "CCL Subscribers" <chemistry-,-ccl.net>

=

To
3D""
"Reichert, David E. " <reichertd-,-= mir.wustl.edu>

cc
3D""

Subject
3D""
CCL: Spherical Micelle Initial Guess (spatial reasonin= g problem)
=3D""3D""<= /td>

Sent to CCL by: "Rajan  Vatassery" [r-vatassery!=3D!= northwestern.edu]
Dear List,
I would like to provide an initial guess for a spherical micelle in or= der to simulate it via MD. I need to place x particles (about 100) on t= he surface of a sphere and they must be equally spaced from one another= . Since there is no analytical solution, I've tried writing a fortran c= ode that would come up with the initial guess from a numerical minimiza= tion. I'm currently having a lot of difficulty with the code and I am h= oping that someone could send me a copy of their code (fortran,c,perl,w= hatever) if they've done this before. Otherwise if someone has an initi= al guess of about 100 particles equally spaced on the surface of a sphe= re (preferably in polar coordinates), I'll gladly take that as well. Th= anks,


raj



-=3D This is automatically added to each message by the mailing script = =3D-
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The "approx" > are done in an 'old fashion' and are for comparison only. > The differences between "static" and "dynamic" pol. are described in > electrodynamics literature, e.g. > BĂttcher, C. J. F. Theory of Electric Polarization: Dielectrics in > Static Fields; Vol 1; Elsevier: Amsterdam, The Netherlands, > 1973. > BĂttcher, C. J. F. Theory of Electric Polarization: Dielectrics > in Time-Dependent Fields; Vol 2; Elsevier: Amsterdam, > The Netherlands, 1978. > static ones (experiment e.g. capacitor) include rotational, vibrational and > electronic polarization (field fequency -> 0). dynamic ones (depending on the > field frequency, experiment e.g. refraction/optical) only electronic > polarization (field frequency >> 0). > The Gaussian polarizability calculations are on the electronic part only. The > standard pol. calc. is on a 'hypothetical' field: zero frequency, but frequency > high enough not to include rotational & vibrational polarization. > Note that you can also do the pol. calc. at an explicit frequency in Gaussian! Thank you for this answer. As far as I understand, the standard polarizability computed by Gaussian98 can be named "dynamic for high frequencies, but not taking into account the inertia of electronic structure". It is interesting, at what interval of frequencies the dynamic polarizabilities are approximately equal to that hypothetical polarizability? > Solvent effects on polarizability are complex & matter of current research. As a > starting review on pol. of ions, you might want to look at our recent article: > A. Serr and R.R. Netz > Polarizabilities of hydrated and free ions derived from DFT calculations > Int. J. Quant. Chem. 106 (12), 2409-2409 (2006) > http://dx.doi.org/10.1002/qua.21121 > Hope this helps, > Andreas Sincerely, Grigoriy Zhurko.