[gmx-users] The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme

Bin Liu fdusuperstring at gmail.com
Thu May 23 21:44:29 CEST 2013

Hi All,

In GROMACS 4.6.x series, Verlet cutoff scheme is introduced to enable
OpenMP parallelization and GPU acceleration. Then some new run parameters
are introduced to control the use of Verlet cutoff scheme. However, I
noticed the GROMACS manual doesn't give in-depth knowledge on some
parameters. For example, I am sure whether and how to use
the coulomb-modifier and vdw-modifier parameters with Verlet cutoff scheme.
My shallow experience told me these two parameters won't affect the
simulation much in term of speed and accuracy. I did a rough benchmark on a
DMPC128 bilayer (323K) system to check the area per lipid against
(traditional) group cutoff scheme results.

Group cutoff scheme: 0.656 (0.008) nm^2   (Uncertainty)

Verlet cutoff scheme (rcoulomb=rvdw=1.0, coulomb-modifier =
Potential-shift-Verlet, vdw-modifier = Potential-shift-Verlet)  0.643nm^2

Verlet cutoff scheme (rcoulomb=rvdw=1.0, coulomb-modifier = None,
vdw-modifier = None)  0.645nm^2

Basically the results from two Verlet cutoff parameter sets are
indistinguishable. I am looking forward to your help to give me some
insight into this question.

Thank you very much.



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