[gmx-users] g_tune_pme scalevdw option not working?

[João Rodrigues]

Checked. Fixed.

Thanks again!

João


2014-03-14 14:03 GMT+01:00 João Rodrigues <anaryin at gmail.com>:

> 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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