[gmx-users] g_tune_pme scalevdw option not working?

[João Rodrigues]

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 <ckutzne at 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 <anaryin at 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 <ckutzne at gwdg.de>:
> >
> >> Dear João,
> >>
> >> On 13 Mar 2014, at 14:38, João Rodrigues <anaryin at 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
> >> --
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