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 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Intra molecular force correction for SPME Message-ID: Content-Type: text/plain; charset=UTF-8 On Jun 4, 2014 10:04 PM, "Sumith YD" 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 > To: Discussion list for GROMACS users > Cc: Discussion list for GROMACS users > > Subject: Re: [gmx-users] Intra molecular force correction for SPME > Message-ID: > > Content-Type: text/plain; charset=UTF-8 > > On Wed, Jun 4, 2014 at 6:52 PM, Sumith YD 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.
[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 To: Discussion list for GROMACS users Cc: Discussion list for GROMACS users Subject: Re: [gmx-users] Intra molecular force correction for SPME Message-ID: Content-Type: text/plain; charset=UTF-8 On Wed, Jun 4, 2014 at 6:52 PM, Sumith YD 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 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". 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. 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.
