Re: [gmx-users] Charges for Coulomb potential
Alright, I understand now. Many thanks for this! Antoine Le 29/08/2012 18:57, Mark Abraham a écrit : On 30/08/2012 3:18 AM, Delmotte, Antoine wrote: Many thanks for your quick response, Mark. So epsilon_r is actually different from the actual relative permittivity (which would be like 80 for water), is that right? You can have an atomistic solvent or a continuum solvent, but not both at once. If so, how does one usually chooses this value of epsilon_r? Is the default value of 1 applicable for most cases (like for simulations in water), or should one obtain it from the literature somehow? The force field defines it (normally to 1). Mark Thank you, Antoine On 29/08/12 14:47, Mark Abraham wrote: On 08/29/2012 11:08 PM, Delmotte, Antoine wrote: Dear Gromacs users, I would like to know which charges are used by Gromacs in the calculation of electrostatic interactions in the standard coulomb potential: E_electrostatics = 138.935 * q1 * q2 / (epsilon_r * r_12); Are q1 and q2 the values tabulated in the file "aminoacids.rtp" of the force field used? If you use pdb2gmx to generate your .top, yes. More generally, GROMACS uses the charges found in the .top. Could you also please redirect me towards the relevant literature for the calculation of epsilon_r in Gromacs? (or does Gromacs uses a fixed epsilon_r?) You choose it. See parts of manual 4.1 and 7.3 Mark -- 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] Charges for Coulomb potential
On 30/08/2012 3:18 AM, Delmotte, Antoine wrote: Many thanks for your quick response, Mark. So epsilon_r is actually different from the actual relative permittivity (which would be like 80 for water), is that right? You can have an atomistic solvent or a continuum solvent, but not both at once. If so, how does one usually chooses this value of epsilon_r? Is the default value of 1 applicable for most cases (like for simulations in water), or should one obtain it from the literature somehow? The force field defines it (normally to 1). Mark Thank you, Antoine On 29/08/12 14:47, Mark Abraham wrote: On 08/29/2012 11:08 PM, Delmotte, Antoine wrote: Dear Gromacs users, I would like to know which charges are used by Gromacs in the calculation of electrostatic interactions in the standard coulomb potential: E_electrostatics = 138.935 * q1 * q2 / (epsilon_r * r_12); Are q1 and q2 the values tabulated in the file "aminoacids.rtp" of the force field used? If you use pdb2gmx to generate your .top, yes. More generally, GROMACS uses the charges found in the .top. Could you also please redirect me towards the relevant literature for the calculation of epsilon_r in Gromacs? (or does Gromacs uses a fixed epsilon_r?) You choose it. See parts of manual 4.1 and 7.3 Mark -- 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] Charges for Coulomb potential
Many thanks for your quick response, Mark. So epsilon_r is actually different from the actual relative permittivity (which would be like 80 for water), is that right? If so, how does one usually chooses this value of epsilon_r? Is the default value of 1 applicable for most cases (like for simulations in water), or should one obtain it from the literature somehow? Thank you, Antoine On 29/08/12 14:47, Mark Abraham wrote: On 08/29/2012 11:08 PM, Delmotte, Antoine wrote: Dear Gromacs users, I would like to know which charges are used by Gromacs in the calculation of electrostatic interactions in the standard coulomb potential: E_electrostatics = 138.935 * q1 * q2 / (epsilon_r * r_12); Are q1 and q2 the values tabulated in the file "aminoacids.rtp" of the force field used? If you use pdb2gmx to generate your .top, yes. More generally, GROMACS uses the charges found in the .top. Could you also please redirect me towards the relevant literature for the calculation of epsilon_r in Gromacs? (or does Gromacs uses a fixed epsilon_r?) You choose it. See parts of manual 4.1 and 7.3 Mark -- 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] Charges for Coulomb potential
On 08/29/2012 11:08 PM, Delmotte, Antoine wrote: Dear Gromacs users, I would like to know which charges are used by Gromacs in the calculation of electrostatic interactions in the standard coulomb potential: E_electrostatics = 138.935 * q1 * q2 / (epsilon_r * r_12); Are q1 and q2 the values tabulated in the file "aminoacids.rtp" of the force field used? If you use pdb2gmx to generate your .top, yes. More generally, GROMACS uses the charges found in the .top. Could you also please redirect me towards the relevant literature for the calculation of epsilon_r in Gromacs? (or does Gromacs uses a fixed epsilon_r?) You choose it. See parts of manual 4.1 and 7.3 Mark -- 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] Charges for Coulomb potential
Dear Gromacs users, I would like to know which charges are used by Gromacs in the calculation of electrostatic interactions in the standard coulomb potential: E_electrostatics = 138.935 * q1 * q2 / (epsilon_r * r_12); Are q1 and q2 the values tabulated in the file "aminoacids.rtp" of the force field used? Could you also please redirect me towards the relevant literature for the calculation of epsilon_r in Gromacs? (or does Gromacs uses a fixed epsilon_r?) Thank you very much in advance, Antoine -- 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
