[gmx-users] g_tune_pme scalevdw option not working?

[João Rodrigues]

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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