Hi João, thanks a lot, I will deal with it tomorrow!
Best, Carsten On 13 Mar 2014, at 18:27, João Rodrigues <anar...@gmail.com> wrote: > Hi Carsten, > > Thanks for the reply and for the info on the rlist modification. > > I created the bug report - http://redmine.gromacs.org/issues/1460 - and > assigned it to you. I also set the priority to low, don't know if it > matters. > > Cheers, > > João > > > 2014-03-13 18:04 GMT+01:00 Carsten Kutzner <ckut...@gwdg.de>: > >> Dear João, >> >> On 13 Mar 2014, at 14:38, João Rodrigues <anar...@gmail.com> wrote: >> >>> Hi all, >>> >>> I've been playing with g_tune_pme (neat tool!) for the last couple of >> days. >>> If I understood correctly, it can also be used to iterate over different >>> rcoulomb values using the -rmin and -rmax options. Using the Verlet >> scheme >>> requires rvdw = rcoulomb, so I used the -scalevdw option (which should be >>> true by default) to keep these equal. This does not seem to happen.. >>> >>> The (partial) contents of a tpr file of such a failed run show the >>> following: >>> >>> verlet-buffer-drift = 0.005 >>> * rlist = 1.213* >>> rlistlong = 1.213 >>> nstcalclr = 15 >>> rtpi = 0.05 >>> coulombtype = PME >>> coulomb-modifier = Potential-shift >>> rcoulomb-switch = 0 >>> * rcoulomb = 1* >>> vdwtype = Cut-off >>> vdw-modifier = Potential-shift >>> rvdw-switch = 0 >>> * rvdw = 1.2* >>> >>> The original mdp has the following parameters: >>> >>> ; Neighborsearching >>> ns_type = grid ; search neighboring grid cels >>> nstlist = 15 ; 10 fs >>> *rlist = 1.2 ; short-range neighborlist cutoff (in >> nm)* >>> *rcoulomb = 1.2 ; short-range electrostatic cutoff (in >> nm)* >>> *rvdw = 1.2 ; short-range van der Waals cutoff (in >> nm)* >>> cutoff-scheme = Verlet >>> >>> ; Electrostatics >>> coulombtype = PME ; Particle Mesh Ewald for long-range >>> electrostatics >>> pme_order = 4 ; cubic interpolation >>> fourierspacing = 0.16 ; grid spacing for FFT >>> >>> I searched a bit in the source code of gmx_tune_pme.c (4.6.5) and found >>> that the only check done between these parameters (rvdw and rcoulomb) is >> if >>> rvdw != rcoulomb in the original file, keep them as is (line 875). Other >>> than that, rvdw is checked against rlist to ensure that it keeps the >>> highest value of the two (rvdw >= rlist) (line 1012). This seems to make >>> sense since rlist was modified based on rcoulomb, in case of plain PME >>> (line 1004). However, this only ensures both values are equal if the new >>> rcoulomb is larger than the original. In case we start with rcoulomb 1.2 >>> and ask g_tune_pme to range from 1.0 to 1.4, those below 1.2 will fail. >> You are right, this is a bug in g_tune_pme. Could you please file this >> issue in http://redmine.gromacs.org and put me as assignee? >> >> Thanks for reporting this! >> >>> Also, why is my rlist changing since it is equal to rcoulomb? It should >> be >>> kept the same (line 1004) right? >> This is a feature of the Verlet scheme, see >> http://www.gromacs.org/Documentation/Cut-off_schemes >> >> Best, >> Carsten >> >> >> >> >> -- >> Dr. Carsten Kutzner >> Max Planck Institute for Biophysical Chemistry >> Theoretical and Computational Biophysics >> Am Fassberg 11, 37077 Goettingen, Germany >> Tel. +49-551-2012313, Fax: +49-551-2012302 >> http://www.mpibpc.mpg.de/grubmueller/kutzner >> http://www.mpibpc.mpg.de/grubmueller/sppexa >> -- >> 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.