[gmx-users] desired usage of verlet-buffer-tolerance with charmm ff?

[Mark Abraham]

Hi,

Note that the reference manual section 3.4.2 talks about this in depth,
plus reports some actual drift numbers. Obviously you should feel free to
observe the drift for yourself!

Historical practice needs to be viewed with an eye also to the use of
charge groups (nobody recommends that any more, and by design the Verlet
scheme can't even do it), and constraints (e.g. SETTLE dominates the energy
drift at some point, so one can't usefully use a large buffer in that very
common case).

Mark

On Thu, 7 Apr 2016 21:55 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?
>
> Thank you,
> Chris.
>
>
>
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