[gmx-users] RE: Neutralising charge distribution
Actually, I'd say they're not incorrect, but incomplete (well, for many systems). There's no mention of the correction terms George was asking about, only the self correction term is taken into account in those equations. But they're in the code allright, and a lot can be induced from the mdp parameters. Jeroen >check the equations in the manual, they are correct (famous >last words...) > >David van der Spoel, Ph.D. ___ 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] RE: Neutralising charge distribution
Hi Jeroen Thanks once again for your reply. Best wishes George -Original Message- From: [EMAIL PROTECTED] on behalf of van Bemmelen Sent: Wed 9/19/2007 11:16 AM To: gmx-users@gromacs.org Subject: [gmx-users] RE: Neutralising charge distribution Hi George, Sorry, I got a bit carried away. Actually, I once thought of somehow taking it out myself, so probably that's why. ;-) About the dipole correction: I haven't experimented with it myself, but I'm pretty sure it's switched off when epsilon_surface is 0. That's also what the manual says (see http://www.gromacs.org/documentation/reference/online/mdp_opt.html#ewald ): "The default value of zero means it is turned off." If you need to be certain about what's exactly going on in the code, you may want to check the function ewald_LRcorrection in the file ewald_util.c. Hope it helps, Jeroen >Date: Wed, 19 Sep 2007 10:40:52 +0100 >From: "Georgios Patargias" <[EMAIL PROTECTED]> >Subject: RE: [gmx-users] RE: Neutralising charge distribution >To: "Discussion list for GROMACS users" >Message-ID: > <[EMAIL PROTECTED]> >Content-Type: text/plain; charset="iso-8859-1" > >Hi Jeroen > >Thank you for your reply. I just wanted to know whether the correction >term for the 'uniform background charge' is included in the >code; I didn't >meant to to take it out. > >Another thing is about the dipole correction that is applied >for conducting >boundary conditions. Is it switched off in PME when >epsilon-surface is 0? > >Regards >George ___ 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
[gmx-users] RE: Neutralising charge distribution
Hi George, Sorry, I got a bit carried away. Actually, I once thought of somehow taking it out myself, so probably that's why. ;-) About the dipole correction: I haven't experimented with it myself, but I'm pretty sure it's switched off when epsilon_surface is 0. That's also what the manual says (see http://www.gromacs.org/documentation/reference/online/mdp_opt.html#ewald ): "The default value of zero means it is turned off." If you need to be certain about what's exactly going on in the code, you may want to check the function ewald_LRcorrection in the file ewald_util.c. Hope it helps, Jeroen >Date: Wed, 19 Sep 2007 10:40:52 +0100 >From: "Georgios Patargias" <[EMAIL PROTECTED]> >Subject: RE: [gmx-users] RE: Neutralising charge distribution >To: "Discussion list for GROMACS users" >Message-ID: > <[EMAIL PROTECTED]> >Content-Type: text/plain; charset="iso-8859-1" > >Hi Jeroen > >Thank you for your reply. I just wanted to know whether the correction >term for the 'uniform background charge' is included in the >code; I didn't >meant to to take it out. > >Another thing is about the dipole correction that is applied >for conducting >boundary conditions. Is it switched off in PME when >epsilon-surface is 0? > >Regards >George ___ 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] RE: Neutralising charge distribution
Georgios Patargias wrote: Hi Jeroen Thank you for your reply. I just wanted to know whether the correction term for the 'uniform background charge' is included in the code; I didn't meant to to take it out. Another thing is about the dipole correction that is applied for conducting boundary conditions. Is it switched off in PME when epsilon-surface is 0? check the equations in the manual, they are correct (famous last words...) Regards George -Original Message- From: [EMAIL PROTECTED] on behalf of van Bemmelen Sent: Tue 9/18/2007 11:14 AM To: gmx-users@gromacs.org Subject: [gmx-users] RE: Neutralising charge distribution Hi George, Yes, such a correction term exists, but it's a divergent term. This term is IMPLICITLY included in the energy, since it compensates for the divergent part in the reciprocal space term, leaving a constant term. This constant term is included explicitly in the code. You could take this constant term out. But be very aware that this constant term not only represents the 'uniform background charge' (or 'neutralising charge distribution', if you will) but also the divergent part of reciprocal space term. So simply leaving it out would be highly unphysical, at least in my opinion. If you really want to know more, I suggest digging into the formulas yourself. :-) Greetz, Jeroen Date: Mon, 17 Sep 2007 16:17:17 +0100 From: "Georgios Patargias" <[EMAIL PROTECTED]> Subject: [gmx-users] Neutralising charge distribution To: Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hello I would like to ask what is the functional form of the uniform neutralising charge distribution applied in Gromacs when doing PME on a charged system. Is there a correction term for this charge distribution that is included in the calculation of energies? Thanks George ___ 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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] RE: Neutralising charge distribution
Hi Jeroen Thank you for your reply. I just wanted to know whether the correction term for the 'uniform background charge' is included in the code; I didn't meant to to take it out. Another thing is about the dipole correction that is applied for conducting boundary conditions. Is it switched off in PME when epsilon-surface is 0? Regards George -Original Message- From: [EMAIL PROTECTED] on behalf of van Bemmelen Sent: Tue 9/18/2007 11:14 AM To: gmx-users@gromacs.org Subject: [gmx-users] RE: Neutralising charge distribution Hi George, Yes, such a correction term exists, but it's a divergent term. This term is IMPLICITLY included in the energy, since it compensates for the divergent part in the reciprocal space term, leaving a constant term. This constant term is included explicitly in the code. You could take this constant term out. But be very aware that this constant term not only represents the 'uniform background charge' (or 'neutralising charge distribution', if you will) but also the divergent part of reciprocal space term. So simply leaving it out would be highly unphysical, at least in my opinion. If you really want to know more, I suggest digging into the formulas yourself. :-) Greetz, Jeroen >Date: Mon, 17 Sep 2007 16:17:17 +0100 >From: "Georgios Patargias" <[EMAIL PROTECTED]> >Subject: [gmx-users] Neutralising charge distribution >To: >Message-ID: > <[EMAIL PROTECTED]> >Content-Type: text/plain; charset="iso-8859-1" > >Hello > >I would like to ask what is the functional form of the uniform >neutralising charge distribution applied in Gromacs when doing >PME on a charged system. > >Is there a correction term for this charge distribution that >is included in the calculation of energies? > >Thanks >George ___ 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
[gmx-users] RE: Neutralising charge distribution
Hi George, Yes, such a correction term exists, but it's a divergent term. This term is IMPLICITLY included in the energy, since it compensates for the divergent part in the reciprocal space term, leaving a constant term. This constant term is included explicitly in the code. You could take this constant term out. But be very aware that this constant term not only represents the 'uniform background charge' (or 'neutralising charge distribution', if you will) but also the divergent part of reciprocal space term. So simply leaving it out would be highly unphysical, at least in my opinion. If you really want to know more, I suggest digging into the formulas yourself. :-) Greetz, Jeroen >Date: Mon, 17 Sep 2007 16:17:17 +0100 >From: "Georgios Patargias" <[EMAIL PROTECTED]> >Subject: [gmx-users] Neutralising charge distribution >To: >Message-ID: > <[EMAIL PROTECTED]> >Content-Type: text/plain; charset="iso-8859-1" > >Hello > >I would like to ask what is the functional form of the uniform >neutralising charge distribution applied in Gromacs when doing >PME on a charged system. > >Is there a correction term for this charge distribution that >is included in the calculation of energies? > >Thanks >George ___ 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
