[gmx-developers] triplet range cut-off

David van der Spoel spoel at xray.bmc.uu.se
Fri Sep 7 08:33:33 CEST 2007

chris.neale at utoronto.ca wrote:
> Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:
>> David van der Spoel wrote:
>>> marcos wrote:
>>>> Hello,
>>>> We are simulating liquid-gas interfaces and we want to include the long
>>>> range forces due to VDW during the course of the simulation. We  
>>>> think to implement a kind of triplet range cut-off. This is to add a
>>>> new (and longer) cut-off to the already existent in the twin-range
>>>> method. This new cut-off will be very long and the forces will be
>>>> updated very infrequently. We plan to apply this only to the VDW  
>>>> interaction, whereas the
>>>> electrostatics will be handled with PME.
>>>> Another possibility is to use a VDW analog of the PME but update the
>>>> forces very rarely.
>>>> Which option do you like more, and where would be the place to start
>>>> modifying the code?
>>> The PME-Van der Waals would be nice to have as an option.
>> Added to wiki project list... weirdly I had thought it was already 
>> there...
> The PME-van der waals would be fantastic. However, I understood that it 
> would be so slow that it is basically not worth doing. I have included 
> posts here in the hopes that somebody can figure out a better way to do 
> it. I believe that "Particle Mesh LJ?" would really be a substantial 
> benifit for lipid bilayers or detergent micelles. Also probably very 
> important for proteins in general.

It would be slow, yes, but the question is how slow? It's probably good 
to consider how important it really is, by quantifying the dispersion 
forces, for instances in a membrane as a function of Z-coordinate by 
varying cut-offs. This can be done without great trouble using a very a 
short mdrun -rerun of an existing trajectory.

I'm pretty confident that the error due to leaving out Van der Waals 
beyond the cut-off, in particular with the dispersion correction turned 
on, is not very large. The obvious problem is the inhomogeneity of the 
system, this can be quantified even easier by summing the C6 terms for 
all atoms over slabs parallel to the membrane, i.e. making a C6 profile 
rather than a density profile.

> see, for example:
> http://www.gromacs.org/pipermail/gmx-users/2007-February/025702.html
> in reply to:
> http://www.gromacs.org/pipermail/gmx-users/2007-February/025700.html
> in reply to:
> http://www.gromacs.org/pipermail/gmx-users/2007-February/025692.html
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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