[gmx-users] The sum of the two largest charge group radii is larger than rlist - rvdw (because rlist < rvdw)

Mark Abraham mark.j.abraham at gmail.com
Tue Feb 26 21:48:17 CET 2013

On Tue, Feb 26, 2013 at 8:56 PM, Christopher Neale <
chris.neale at mail.utoronto.ca> wrote:

> Dear users:
> I am experimenting with the "Stockholm" lipid parameters (Slipids). I
> downloaded the recommended .mdp file from the developers of this force
> field ( http://people.su.se/~jjm/Stockholm_Lipids/Downloads_files/md.mdp) and was surprised to see the treatment of non-bonded interactions:
> coulombtype = pme
> rcoulomb = 1.0
> rlist = 1.0
> rlistlong = 1.6
> rvdw = 1.5
> rvdw-switch = 1.4
> vdw-type = switch
> it struck me as strange to have rlist < rvdw (I didn't even know that this
> was allowed, but I tried it and it is)

Yup, that's what twin-range does.

(Note that this is from their website, but their original paper would have
> used rcoulomb = 1.4 and rlist = 1.4).
> When I run grompp version 4.5.5 with these parameters, I get the following
> note:
> NOTE 2 [file empty.mdp]:
>   The sum of the two largest charge group radii (0.000000) is larger than
>   rlist (1.000000) - rvdw (1.500000)
> This system has only one Na and one Cl ion (chosen for simplicity during
> mdp testing). By moving these ions apart and doing a 0-step mdrun, I was
> able to verify that the LJ interaction energy moves from the LJ(SR) to the
> LJ(LR) component for d>=1 nm and that this energy is non-zero until d>=1.5
> nm.
> I am asking if anybody sees a problem because (a) grompp threw a note, and
> (b) even if this works alright for standard simulations, I just want to be
> sure that if I get into more exotic parts of the gromacs code then I am not
> likely to encounter situations in which this cutoff scheme introduces
> problems (silent or otherwise).

It seems there's some issue with how that note is being triggered that
bears investigation, in case there's further problems to uncover. Can you
attach a tarball of grompp inputs to http://redmine.gromacs.org/issues/1164,
please? (It may or may not be the same issue as that one, but they may as
well be investigated together!)


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