[gmx-users] The effect of coulomb-modifier and vdw-modifier in Verlet cutoff scheme
mark.j.abraham at gmail.com
Thu May 23 22:11:49 CEST 2013
Those modifiers shift only the potential, as manual 7.3 points out. So the
forces and sampling are unaffected, so it does not surprise me that APL is
unaffected by the use of such a shift. If your group cutoff scheme was
unbuffered (rlist <= max(rcoulcomb,rvdw) and nstlist > 1), then if the
observed difference is significant, then that could be the reason.
On Thu, May 23, 2013 at 9:44 PM, Bin Liu <fdusuperstring at gmail.com> wrote:
> 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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