Re: [gmx-users] Polarizability
Hi, there's a very recent paper of the GROMOS team, where they evaluate the free energy of polarization (with the 'Charge-on-Spring' model): http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/asap/abs/jp0706477.html Their code is already working, but under the GROMOS software... Ciao, Patrick Jones de Andrade a écrit : Hi David They have published a few paper on water and alcohols. The charm crew have done a few more. Amber is actually split into two IIRC, with point dipoles as well as shell models (that means either or). I've found two papers for charmm polariability. But I'll only be able to try to find it in the library or to ask for the authors tomorrow at least. But thanks for the information! ;) On the other hand, I could not yet find any published material from amber using shell models. Is this only an inside group discussion? I think there is not a lot of difference, but shell models are easier to implement. I think too. In reality, there is no visible rational reason for this fear of me, is more like a feeling, so I'll try to find something more on it. But I do agree that it's much likely that the shell model is much easier to implement, if not faster to execute also. :) I am working on shell models a bit (not enough...) Me too. Specially cause this is long terms plans (2+ years from now). But thanks a lot for all information, David. Helped a lot. Sincerally yours, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Polarizability
Hi Jones, Charge-on-spring model is another name for shell model. Here's what's written in the introduction of the paper: [...]in the charge-on-spring (or Drude-oscillator or shell) model, an additional point charge is attached to a polarizable center that can adapt its position to the electric field to induce a net dipole.[...] Ciao, Patrick Jones de Andrade a écrit : Hi Patrick. Just got this paper here, thanks for the indication. This may sound like a dumb question, but: am I wrong, or the shell model and the charge on a spring model differ only by the fact that the VdW interation is also floating aroung in the shell model but not in the charge on a spring one? Thanks a lot, Jones On 5/21/07, *Patrick Fuchs* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Hi, there's a very recent paper of the GROMOS team, where they evaluate the free energy of polarization (with the 'Charge-on-Spring' model): http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/asap/abs/jp0706477.html http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/asap/abs/jp0706477.html Their code is already working, but under the GROMOS software... Ciao, Patrick Jones de Andrade a écrit : Hi David They have published a few paper on water and alcohols. The charm crew have done a few more. Amber is actually split into two IIRC, with point dipoles as well as shell models (that means either or). I've found two papers for charmm polariability. But I'll only be able to try to find it in the library or to ask for the authors tomorrow at least. But thanks for the information! ;) On the other hand, I could not yet find any published material from amber using shell models. Is this only an inside group discussion? I think there is not a lot of difference, but shell models are easier to implement. I think too. In reality, there is no visible rational reason for this fear of me, is more like a feeling, so I'll try to find something more on it. But I do agree that it's much likely that the shell model is much easier to implement, if not faster to execute also. :) I am working on shell models a bit (not enough...) Me too. Specially cause this is long terms plans (2+ years from now). But thanks a lot for all information, David. Helped a lot. Sincerally yours, Jones ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs http://www.ebgm.jussieu.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs
Re: [gmx-users] Polarizability
Jones de Andrade wrote: Hi list. Well, a few days ago I've written a message concerning the future implementations that could be expected min gromacs 4 when it's released. Unfortunatelly, the thread hasn't gone any further. lots of plans, but no promises. we really don't want to raise any expectations, more than significantly increased performance both sequential and parallel. So, I would like to know if there is somone in this list who ever tried to modify gromacs program forces and energies routines. More specifically, if someone has tried to somehow implement any polarizability model in the force field, other than the shells model. no plans. the shell model will most likely be the dominant model, both gromos and charmm developers are using it now. if you feel like implementing other stuff yourself, you're welcome to continue the discussion on the developer list. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Polarizability
Hi David. I had no idea that gromos was using it. Also, just had a few clues that maybe charmm was. All amber clues however points towards a different model. I have a few concerns about directioning (really sure that this is the wrong word, if exists) that a shell model polarizability would make. Absolutely no doubts that it would be probably faster than any iterative model include dipoles, but I have this concern. I'll be looking forward for the charmm papers on it (I've found the references late this week) and try to compare its reproducibility and parametrization methodologies somehow. About implementing it: its a good idea, but a long term one. Basically it means that nobody in the developer's list seems to be working on it righ now, right? ;) Thanks a lot for all answers, David. :) Sincerally yours, Jones On 5/20/07, David van der Spoel [EMAIL PROTECTED] wrote: Jones de Andrade wrote: Hi list. Well, a few days ago I've written a message concerning the future implementations that could be expected min gromacs 4 when it's released. Unfortunatelly, the thread hasn't gone any further. lots of plans, but no promises. we really don't want to raise any expectations, more than significantly increased performance both sequential and parallel. So, I would like to know if there is somone in this list who ever tried to modify gromacs program forces and energies routines. More specifically, if someone has tried to somehow implement any polarizability model in the force field, other than the shells model. no plans. the shell model will most likely be the dominant model, both gromos and charmm developers are using it now. if you feel like implementing other stuff yourself, you're welcome to continue the discussion on the developer list. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Polarizability
Jones de Andrade wrote: Hi David. I had no idea that gromos was using it. Also, just had a few clues that maybe charmm was. All amber clues however points towards a different model. They have published a few paper on water and alcohols. The charm crew have done a few more. Amber is actually split into two IIRC, with point dipoles as well as shell models (that means either or). I have a few concerns about directioning (really sure that this is the wrong word, if exists) that a shell model polarizability would make. Absolutely no doubts that it would be probably faster than any iterative model include dipoles, but I have this concern. I think there is not a lot of difference, but shell models are easier to implement. I'll be looking forward for the charmm papers on it (I've found the references late this week) and try to compare its reproducibility and parametrization methodologies somehow. About implementing it: its a good idea, but a long term one. Basically it means that nobody in the developer's list seems to be working on it righ now, right? ;) I am working on shell models a bit (not enough...) Thanks a lot for all answers, David. :) Sincerally yours, Jones -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Polarizability
Hi list. Well, a few days ago I've written a message concerning the future implementations that could be expected min gromacs 4 when it's released. Unfortunatelly, the thread hasn't gone any further. So, I would like to know if there is somone in this list who ever tried to modify gromacs program forces and energies routines. More specifically, if someone has tried to somehow implement any polarizability model in the force field, other than the shells model. I'm deeply interested in it. Thanks a lot in advance, sincerally yours, Jones ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
