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

Christopher Neale chris.neale at mail.utoronto.ca
Tue Feb 26 20:56:12 CET 2013

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)

(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).

Thank you,

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