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

Christopher Neale chris.neale at alum.utoronto.ca
Thu Apr 7 21:55:29 CEST 2016

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,

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