[gmx-users] g_tune_pme scalevdw option not working?

[Carsten Kutzner]

Hi João,

thanks a lot, I will deal with it tomorrow!

Best,
 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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