[gmx-users] The sum of the two largest charge group radii is larger than rlist - rvdw (because rlist < rvdw)
chris.neale at mail.utoronto.ca
Thu Feb 28 05:44:15 CET 2013
I've started bilayer simulations with both of the new conditions that you mentioned. Thank you for the advice ans references. I am surprised to hear that the bilayer features are similar with different vdw cutoffs (although I'll check also). Perhaps this is an unexpected win for dispersion correction. Michael Shirts, et al., continue to show us the importance/usefulness of dispersion correction in aqueous solution, but I was surprised to hear that it also seems to work better than one might hope for when simulating orientationally anisotropic biphasic systems like a bilayer in water.
Thanks for your input,
-- original message --
We have used the following settings in our recent work (http://pubs.rsc.org/en/content/articlelanding/2013/CP/C3CP44472D):
And this works fine without any notes etc from grompp, and you do not have to use the switching function. Should probably change the md.mdp file on the website...thanks for bringing this to our attention!
A colleague of mine have used Slipids with a shorter rvdw and the bilayer properties were still very stable. When I use rcoulomb=rvdw=1.0 I see no major difference either except for a relatively big boost in performance. But please double check that your simulations are able to reproduce experimental observables if changing rvdw to around 1.0 nm., but it should be fine.
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