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

[Mark Abraham]

If one is using the potential for something (e.g. reweighting, replica
exchange) then now the possibility of a systematic deviation with shifted
potentials is real.

Mark


On Thu, May 23, 2013 at 10:11 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> 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.
>
> Mark
>
>
>
> 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.
>>
>> Regards
>>
>> Bin
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>
>