[gmx-users] g_tune_pme scalevdw option not working?
ckutzne at gwdg.de
Thu Mar 13 18:05:32 CET 2014
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
> 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
> 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
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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