[gmx-users] g_tune_pme scalevdw option not working?
ckutzne at gwdg.de
Thu Mar 13 19:21:28 CET 2014
thanks a lot, I will deal with it tomorrow!
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
> 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
>>> If I understood correctly, it can also be used to iterate over different
>>> rcoulomb values using the -rmin and -rmax options. Using the Verlet
>>> 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
>>> 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
>>> *rcoulomb = 1.2 ; short-range electrostatic cutoff (in
>>> *rvdw = 1.2 ; short-range van der Waals cutoff (in
>>> cutoff-scheme = Verlet
>>> ; Electrostatics
>>> coulombtype = PME ; Particle Mesh Ewald for long-range
>>> 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
>>> 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
>>> kept the same (line 1004) right?
>> This is a feature of the Verlet scheme, see
>> 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
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