Re: [gmx-users] Intra molecular force correction for SPME
On Jun 4, 2014 10:04 PM, Sumith YD ydsum...@gmail.com wrote: Dear Mark, For the paper please refer http://www.ii.uib.no/~matthey/text/mattheyPhD.pdf;. That's just restating standard stuff, e.g. Essman 1995. While calculating the forces in SPC/E water, H-O, H-H forces in the same molecule will be calculated in reciprocal space due to the property of Particle Mesh technique. Do you mean to say that this will be compensated by SHAKE/SETTLE? Won't it affect the net force acting on the molecule if we don't remove it? I thought you were referring to larger rigid bodies. Bonded exclusions are dealt with by all these codes the same way. Note carefully the use of erf vs erfc in the corrective terms. Mark Sumith YD Date: Wed, 4 Jun 2014 21:26:31 +0200 From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Cc: Discussion list for GROMACS users gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Intra molecular force correction for SPME Message-ID: CAMNuMATfDXtbztpO8isPubzU709mDkjLLv3s= tr5ex0jdn3...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 On Wed, Jun 4, 2014 at 6:52 PM, Sumith YD ydsum...@gmail.com wrote: Dear gromacs community, How does the gromacs calculate Intra molecular force correction (To correct the unwanted intra molecular force in Fourier space especially for rigid molecules)? I couldn't find that information listed anywhere in the manual. I could find some details from Publications by Thierry Matthey- PhD thesis. Where is that? But I couldn't find gromacs citing it and hence just curious to know is there any other reference which gromacs uses? I am also having a hard time to locate intramolecular force correction in the source code. I tried the mail archive and Google search but couldn't exactly locate/find anything helpful. Pardon me if this question was asked earlier and answered. GROMACS doesn't implement rigid molecules except inasmuch as they can be expressed through holonomic constraints on bonds and angles (or frozen atoms). As such, the forces are projected out (respectively, zeroed), so the question does not arise. Mark Sumith Mechanical Engineer, Syracuse University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Intra molecular force correction for SPME
Dear Mark, Thank you so much for the clarification. I will try to locate that equation in the source code too. Sumith YD. Date: Thu, 5 Jun 2014 20:43:03 +0200 From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Subject: Re: [gmx-users] Intra molecular force correction for SPME Message-ID: camnumarodamxrqbd5cnoif8uskapcv56+feop5w7qnng0qp...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 On Jun 4, 2014 10:04 PM, Sumith YD ydsum...@gmail.com wrote: Dear Mark, For the paper please refer http://www.ii.uib.no/~matthey/text/mattheyPhD.pdf;. That's just restating standard stuff, e.g. Essman 1995. While calculating the forces in SPC/E water, H-O, H-H forces in the same molecule will be calculated in reciprocal space due to the property of Particle Mesh technique. Do you mean to say that this will be compensated by SHAKE/SETTLE? Won't it affect the net force acting on the molecule if we don't remove it? I thought you were referring to larger rigid bodies. Bonded exclusions are dealt with by all these codes the same way. Note carefully the use of erf vs erfc in the corrective terms. Mark Sumith YD Date: Wed, 4 Jun 2014 21:26:31 +0200 From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Cc: Discussion list for GROMACS users gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Intra molecular force correction for SPME Message-ID: CAMNuMATfDXtbztpO8isPubzU709mDkjLLv3s= tr5ex0jdn3...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 On Wed, Jun 4, 2014 at 6:52 PM, Sumith YD ydsum...@gmail.com wrote: Dear gromacs community, How does the gromacs calculate Intra molecular force correction (To correct the unwanted intra molecular force in Fourier space especially for rigid molecules)? I couldn't find that information listed anywhere in the manual. I could find some details from Publications by Thierry Matthey- PhD thesis. Where is that? But I couldn't find gromacs citing it and hence just curious to know is there any other reference which gromacs uses? I am also having a hard time to locate intramolecular force correction in the source code. I tried the mail archive and Google search but couldn't exactly locate/find anything helpful. Pardon me if this question was asked earlier and answered. GROMACS doesn't implement rigid molecules except inasmuch as they can be expressed through holonomic constraints on bonds and angles (or frozen atoms). As such, the forces are projected out (respectively, zeroed), so the question does not arise. Mark Sumith Mechanical Engineer, Syracuse University. -- -- thanks regards, Sumith YD -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Intra molecular force correction for SPME
ewald_LRcorrection in gmxlib/ewald_util.c (for the group scheme). Aliens probably handle it for the Verlet scheme, for all I know ;-) Mark On Thu, Jun 5, 2014 at 9:15 PM, Sumith YD ydsum...@gmail.com wrote: Dear Mark, Thank you so much for the clarification. I will try to locate that equation in the source code too. Sumith YD. Date: Thu, 5 Jun 2014 20:43:03 +0200 From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Subject: Re: [gmx-users] Intra molecular force correction for SPME Message-ID: camnumarodamxrqbd5cnoif8uskapcv56+feop5w7qnng0qp...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 On Jun 4, 2014 10:04 PM, Sumith YD ydsum...@gmail.com wrote: Dear Mark, For the paper please refer http://www.ii.uib.no/~matthey/text/mattheyPhD.pdf;. That's just restating standard stuff, e.g. Essman 1995. While calculating the forces in SPC/E water, H-O, H-H forces in the same molecule will be calculated in reciprocal space due to the property of Particle Mesh technique. Do you mean to say that this will be compensated by SHAKE/SETTLE? Won't it affect the net force acting on the molecule if we don't remove it? I thought you were referring to larger rigid bodies. Bonded exclusions are dealt with by all these codes the same way. Note carefully the use of erf vs erfc in the corrective terms. Mark Sumith YD Date: Wed, 4 Jun 2014 21:26:31 +0200 From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Cc: Discussion list for GROMACS users gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Intra molecular force correction for SPME Message-ID: CAMNuMATfDXtbztpO8isPubzU709mDkjLLv3s= tr5ex0jdn3...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 On Wed, Jun 4, 2014 at 6:52 PM, Sumith YD ydsum...@gmail.com wrote: Dear gromacs community, How does the gromacs calculate Intra molecular force correction (To correct the unwanted intra molecular force in Fourier space especially for rigid molecules)? I couldn't find that information listed anywhere in the manual. I could find some details from Publications by Thierry Matthey- PhD thesis. Where is that? But I couldn't find gromacs citing it and hence just curious to know is there any other reference which gromacs uses? I am also having a hard time to locate intramolecular force correction in the source code. I tried the mail archive and Google search but couldn't exactly locate/find anything helpful. Pardon me if this question was asked earlier and answered. GROMACS doesn't implement rigid molecules except inasmuch as they can be expressed through holonomic constraints on bonds and angles (or frozen atoms). As such, the forces are projected out (respectively, zeroed), so the question does not arise. Mark Sumith Mechanical Engineer, Syracuse University. -- -- thanks regards, Sumith YD -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Intra molecular force correction for SPME
On Wed, Jun 4, 2014 at 6:52 PM, Sumith YD ydsum...@gmail.com wrote: Dear gromacs community, How does the gromacs calculate Intra molecular force correction (To correct the unwanted intra molecular force in Fourier space especially for rigid molecules)? I couldn't find that information listed anywhere in the manual. I could find some details from Publications by Thierry Matthey- PhD thesis. Where is that? But I couldn't find gromacs citing it and hence just curious to know is there any other reference which gromacs uses? I am also having a hard time to locate intramolecular force correction in the source code. I tried the mail archive and Google search but couldn't exactly locate/find anything helpful. Pardon me if this question was asked earlier and answered. GROMACS doesn't implement rigid molecules except inasmuch as they can be expressed through holonomic constraints on bonds and angles (or frozen atoms). As such, the forces are projected out (respectively, zeroed), so the question does not arise. Mark Sumith Mechanical Engineer, Syracuse University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Intra molecular force correction for SPME
Dear Mark, For the paper please refer http://www.ii.uib.no/~matthey/text/mattheyPhD.pdf;. While calculating the forces in SPC/E water, H-O, H-H forces in the same molecule will be calculated in reciprocal space due to the property of Particle Mesh technique. Do you mean to say that this will be compensated by SHAKE/SETTLE? Won't it affect the net force acting on the molecule if we don't remove it? Sumith YD Date: Wed, 4 Jun 2014 21:26:31 +0200 From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Cc: Discussion list for GROMACS users gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Intra molecular force correction for SPME Message-ID: CAMNuMATfDXtbztpO8isPubzU709mDkjLLv3s=tr5ex0jdn3...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 On Wed, Jun 4, 2014 at 6:52 PM, Sumith YD ydsum...@gmail.com wrote: Dear gromacs community, How does the gromacs calculate Intra molecular force correction (To correct the unwanted intra molecular force in Fourier space especially for rigid molecules)? I couldn't find that information listed anywhere in the manual. I could find some details from Publications by Thierry Matthey- PhD thesis. Where is that? But I couldn't find gromacs citing it and hence just curious to know is there any other reference which gromacs uses? I am also having a hard time to locate intramolecular force correction in the source code. I tried the mail archive and Google search but couldn't exactly locate/find anything helpful. Pardon me if this question was asked earlier and answered. GROMACS doesn't implement rigid molecules except inasmuch as they can be expressed through holonomic constraints on bonds and angles (or frozen atoms). As such, the forces are projected out (respectively, zeroed), so the question does not arise. Mark Sumith Mechanical Engineer, Syracuse University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
