[gmx-users] desired usage of verlet-buffer-tolerance with charmm ff?
pall.szilard at gmail.com
Fri Apr 8 12:42:14 CEST 2016
On Thu, Apr 7, 2016 at 9:55 PM, Christopher Neale
<chris.neale at alum.utoronto.ca> wrote:
> Dear users:
> Charmm mdp options are listed here: http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM with the following values:
> constraints = h-bonds
> cutoff-scheme = Verlet
> vdwtype = cutoff
> vdw-modifier = force-switch
> rlist = 1.2
> rvdw = 1.2
> rvdw-switch = 1.0
> coulombtype = PME
> rcoulomb = 1.2
> DispCorr = no
> ;; verlet-buffer-tolerance is not included in that list , so I presume the suggestion is to accept the default value of 0.005 kJ/mol/ps
> However, I would have expected:
> rlist = 1.4
> verlet-buffer-tolerance = -1
> I realize that issue #1413 ( http://redmine.gromacs.org/issues/1413 ) is still open, but when I use the approach suggested at http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM I get a surprisingly small increase in rlist as nstlist is increased:
> Reading file MD.tpr, VERSION 5.1.2 (single precision)
> Changing nstlist from 10 to 25, rlist from 1.2 to 1.207
> I read somewhere that there is buffering in the verlet scheme, but 0.007 nm sure doesn't seem like a lot... I must be missing something?
What you are missing is likely that the Verlet scheme uses a
particle-cluster based approach where the pair ("neighbor") list is
built of such clusters. This provides an implicit buffer which is
always present even when rcut=rlist and therefore the explicit buffer
can be kept shorter.
See e.g. Fig 3 of , the blue non filled atoms represent the implicit buffer.
> Thank you,
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