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.