[gmx-users] correct rlist and Verlet scheme

Hardy, Adam ah259 at hw.ac.uk
Fri Feb 12 13:56:02 CET 2016

There are people more qualified than me to explain the fine details of this, but in brief:

Verlet on it's own doesn't adjust rvdw or rcoloumb (rcoulomb may be adjusted if you rae using PME for the coulomb interactions), but by default it will adjust the neighbour list cut-off (rlist) to remain with a specified energy tolerance given by verlet-buffer-tolerance. You can overide this behaviour and manually set rlist by setting verlet-buffer-tolerance=-1. Whether you want to or not will depend on why the forcefield has specified that cut-off, it may well be to achieve the same purpose, which is to propely catch interactions between atoms which move in or out of the cut-off radii between rlist update steps.


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Timofey Tyugashev <tyugashev at niboch.nsc.ru>
Sent: 12 February 2016 12:47
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] correct rlist and Verlet scheme

I have trouble in correctly setting cut-offs with Verlet scheme to match
force-field specific settings.
It automatically adjusts cut-off and it looks like they change their
values from ones recommended for the force field.
Is there a way to correct it and set up them properly?

The paper on FF lists 1.0 nm for short-range electrostatic and LJ
The cut-off of pairlists is 1.05 nm.

The forcefield is 99SB-ILDN and is present in GROMACS itself.
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