[gmx-users] Non-bonded interactions settings using Amber

Dawid das addiw7 at googlemail.com
Fri Sep 6 17:20:53 CEST 2019

Dear All,

I am using amber99fb-star-ildn with Gromacs2016.3 and I'm not sure how to
choose some options for non-bonded interactions such as

vdw-modifier (potential-shift or potential-shift-verlet or potential-switch)
dispcorr (EnerPres or no)

I read original papers about amber99fb, amber99fb-star and amber99fb-ildn
but the choice of rcoulomb and rvdw was always different so I got confused.
I was expecting that when I use amber ff I need to use very specific
options as suggested for charmm ff on Gromacs website but I couldn't find
similar tips for the amber.

I found a topic on this mailing list that somehow answers my question,
namely that the choice of cut-off radii is not so strict in case of amber
force fields. On the other hand I remember that Dr Lemkul wrote on
a number of occasions that cut-off is part of a force field so now I'm
not really sure how to choose all those parameters to get meaningful

Best wishes,
Dawid Grabarek

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