Re: [gmx-users] BD with Hydrodynamic interactions?
On Sun, 2011-09-25 at 14:03 -0700, Sanku M wrote: Hi, I was wondering whether BD simulation integrator in Gromacs also have option of including hydrodynamic interactions. Hello, I do not think, that Gromacs has something like Lattice-Boltzmann implemented so far. Furthermore you would need a momentum-conserving method for the calculation of the electrostatic forces, which is not given with the analytical differentiation of SPME, that conserves only energy and not momentum. /Flo Sanku -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[Fwd: Re: [gmx-users] BD with Hydrodynamic interactions?]
Forwarded Message From: Sanku M msank...@yahoo.com Reply-to: Sanku M msank...@yahoo.com To: Dommert Florian domm...@icp.uni-stuttgart.de Subject: Re: [gmx-users] BD with Hydrodynamic interactions? Date: Mon, 26 Sep 2011 04:07:38 -0700 (PDT) I did not mean lattice boltzmann by BD. By BD I meant Brownian Dynamics. In general, for accuracy in dynamics, one uses hydrodynamic interaction in brownian dynamics simulation. I was wondering whether hydrodynamic interaction is invoked in gromacs implementation of brownian dynamics simulation. Please keep correspondence on the mailing list. So how do want to include hydrodynamic interactions into BD ? I think the Lattice-Boltzmann method is a way to do this isn't it ? /Flo From: Dommert Florian domm...@icp.uni-stuttgart.de To: Sanku M msank...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, September 26, 2011 3:38 AM Subject: Re: [gmx-users] BD with Hydrodynamic interactions? On Sun, 2011-09-25 at 14:03 -0700, Sanku M wrote: Hi, I was wondering whether BD simulation integrator in Gromacs also have option of including hydrodynamic interactions. Hello, I do not think, that Gromacs has something like Lattice-Boltzmann implemented so far. Furthermore you would need a momentum-conserving method for the calculation of the electrostatic forces, which is not given with the analytical differentiation of SPME, that conserves only energy and not momentum. /Flo Sanku -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] BD with Hydrodynamic interactions?
I did not mean lattice boltzmann by BD. By BD I meant Brownian Dynamics. In general, for accuracy in dynamics, one uses hydrodynamic interaction in brownian dynamics simulation. I was wondering whether hydrodynamic interaction is invoked in gromacs implementation of brownian dynamics simulation. From: Sanku M msank...@yahoo.com To: Dommert Florian domm...@icp.uni-stuttgart.de Sent: Monday, September 26, 2011 6:07 AM Subject: Re: [gmx-users] BD with Hydrodynamic interactions? I did not mean lattice boltzmann by BD. By BD I meant Brownian Dynamics. In general, for accuracy in dynamics, one uses hydrodynamic interaction in brownian dynamics simulation. I was wondering whether hydrodynamic interaction is invoked in gromacs implementation of brownian dynamics simulation. From: Dommert Florian domm...@icp.uni-stuttgart.de To: Sanku M msank...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, September 26, 2011 3:38 AM Subject: Re: [gmx-users] BD with Hydrodynamic interactions? On Sun, 2011-09-25 at 14:03 -0700, Sanku M wrote: Hi, I was wondering whether BD simulation integrator in Gromacs also have option of including hydrodynamic interactions. Hello, I do not think, that Gromacs has something like Lattice-Boltzmann implemented so far. Furthermore you would need a momentum-conserving method for the calculation of the electrostatic forces, which is not given with the analytical differentiation of SPME, that conserves only energy and not momentum. /Flo Sanku -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] BD with Hydrodynamic interactions?
On 26/09/2011 11:59 PM, Sanku M wrote: I did not mean lattice boltzmann by BD. By BD I meant Brownian Dynamics. In general, for accuracy in dynamics, one uses hydrodynamic interaction in brownian dynamics simulation. I was wondering whether hydrodynamic interaction is invoked in gromacs implementation of brownian dynamics simulation. The manual section of BD doesn't mention it, so very probably not. Mark *From:* Sanku M msank...@yahoo.com *To:* Dommert Florian domm...@icp.uni-stuttgart.de *Sent:* Monday, September 26, 2011 6:07 AM *Subject:* Re: [gmx-users] BD with Hydrodynamic interactions? I did not mean lattice boltzmann by BD. By BD I meant Brownian Dynamics. In general, for accuracy in dynamics, one uses hydrodynamic interaction in brownian dynamics simulation. I was wondering whether hydrodynamic interaction is invoked in gromacs implementation of brownian dynamics simulation. *From:* Dommert Florian domm...@icp.uni-stuttgart.de *To:* Sanku M msank...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Monday, September 26, 2011 3:38 AM *Subject:* Re: [gmx-users] BD with Hydrodynamic interactions? On Sun, 2011-09-25 at 14:03 -0700, Sanku M wrote: Hi, I was wondering whether BD simulation integrator in Gromacs also have option of including hydrodynamic interactions. Hello, I do not think, that Gromacs has something like Lattice-Boltzmann implemented so far. Furthermore you would need a momentum-conserving method for the calculation of the electrostatic forces, which is not given with the analytical differentiation of SPME, that conserves only energy and not momentum. /Flo Sanku -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de mailto:domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert http://www.icp.uni-stuttgart.de/%7Eicp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] BD with Hydrodynamic interactions?
Hi, I was wondering whether BD simulation integrator in Gromacs also have option of including hydrodynamic interactions. Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
