Hi Carsten, Thanks for the fix!
Will run it today and get back to you with the results. Cheers, João 2014-03-14 12:32 GMT+01:00 Carsten Kutzner <ckut...@gwdg.de>: > Dear João, > > could you check whether > > https://gerrit.gromacs.org/#/c/3267/ > > fixes your problems with g_tune_pme? > > Thanks, > 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? 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