[gmx-developers] modifing nonbonded interactions

Mark Abraham Mark.Abraham at anu.edu.au
Sun Oct 19 11:29:50 CEST 2008

David van der Spoel wrote:
> Nazish Hoda wrote:
>>> OK. While the simplest way to implement this is to modify the inner 
>>> loop of the kernels to do such a comparison, this will severely hurt 
>>> performance. If one was already dropping from the optimized kernels 
>>> to a generic kernel, then the additional drop is probably not so 
>>> severe, but I'd expect still noticeable.
>> This is what I have done. It is definetely slower. I am more 
>> interested in checking the physics. If this works then I will think of 
>> implementing the other idea you gave; that would require more effort. 
>> The big plan is to perform implict solvent simulations for charged 
>> systems that can mimic full atomistic simulations.
>> I have posted these queries on a regular basis for two weeks now, 
>> since I started to work on this. But no one use to respond. I did not 
>> wanted to
>> spend much time going through the full source code because I needed to
>> add just few lines. I was lucky today that I got some responses.
>> I would like to thank you once more, it really saved me lots of time, 
>> Nazish.
> Implementing distance dependent cutoff using tables is very simple, in 
> addition it does not hurt performance compared to e.g.using PME since 
> you we use tables for that as well. Most important using tables this 
> will work in vanilla gromacs.
> You may want to check recent papers by Berk Hess where he has done 
> similar things, by the way.

/headslap... of course, David is right!


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