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.