[gmx-developers] triplet range cut-off

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Sep 7 19:02:56 CEST 2007

Quoting Erik Lindahl <lindahl at cbr.su.se>:

> Hi,
> On Sep 6, 2007, at 11:33 PM, David van der Spoel wrote:
>>>> 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.
> That thought has actually crossed my mind to - doing anisotropic
> dispersion corrections.
> I won't rule out implementing LJ-PME, and I guess there are a couple of
> optimizations we could do, e.g. optionally assume geometric combination
> rules for the reciprocal space part. At least in theory it could also
> make it possible to use very short direct-space cutoffs (0.5nm), but
> that doesn't go too well with the new domain decomposition at the
> moment.
> However, before embarking on it I agree we need to see a couple of
> examples that quantify the improvement you get from long LJ :-)

I would be happy to look into this after I get back from vacation on  
the 1st of October. The suggestions above for a test system sound  
appropriate. If anybody comes up with other good ideas for a test  
system, please let me know.

> Cheers,
> Erik
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