[gmx-users] correct rlist and Verlet scheme

[Mark Abraham]

Hi,

As Adam says, you want to understand the reason why the forcefield
specifies the settings it does. For example, until at least AMBER 2003,
their force field papers did not specify PME parameters more precisely than
"x nm cutoff was used." If PME was used at all. ;-) So you can be guided
also by the parameters reported by successful users of these forcefields,
particularly those of the various force field and software authors.

rlist is a free parameter so long as you choose it large enough to avoid
missing a significant number of interactions over the lifetime of the list
- but it affects performance strongly. rcoulomb can be varied for
equivalent accuracy if matching changes occur to PME parameters. VDW
parameters should generally follow the force field derivation precisely
(but add long-range corrections for dispersion) - GROMACS will not change
these. You should check out the background information in the reference
manual, sections 3.4.2 and 3.17.5

Mark

On Fri, Feb 12, 2016 at 1:56 PM Hardy, Adam <ah259 at hw.ac.uk> wrote:

> 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.
>
> Adam
>
> ________________________________________
> 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
> interactions.
> The cut-off of pairlists is 1.05 nm.
>
> The forcefield is 99SB-ILDN and is present in GROMACS itself.
> --
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