[gmx-users] g_tune_pme scalevdw option not working?

[Carsten Kutzner]

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