[gmx-developers] modifing nonbonded interactions

[Nazish Hoda]

Hi David,

Can you tell me which journal and where was this paper published ?

Thanks, Nazish.



Quoting David van der Spoel <spoel at xray.bmc.uu.se>:

> 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.
>
>>
>>
>> Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:
>>
>>> Nazish Hoda wrote:
>>>> Hi Mark,
>>>>
>>>> I really appreciate your help.
>>>> Let me first describe what I am planning to do.
>>>> I want to implement a position dependent dielectric constant:
>>>> \epsilon = \epsilon_near  r < r_1,
>>>> \epsilon = \epsilon_far   r > r_1.
>>>
>>> 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.
>>>
>>> Much better would be to hijack the twin-range cut-off machinery to  
>>> create different groups of nonbonded interactions which get sent  
>>> to unmodified nonbonded kernels with different epsilon values.  
>>> This way the  distance test is done once per (charge-group)  
>>> interaction during the neighbour-searching, and you get to keep  
>>> the optimized kernels. See section 4.6.3 of the GROMACS 3.3 manual  
>>> for some introductory information.
>>>
>>> Better still would be to find that some other simulation code  
>>> already has such a mechanism implemented.
>>>
>>>> Regarding your suggestions, I now understand that I can force it  
>>>> not to use the optimized subroutines. Though I did not undertand  
>>>> what David means that I will be better served by using lookup  
>>>> tables; is he referring to the numbering scheme for LJ,  
>>>> Coloumbic, and water optimized functions, and how to use this  
>>>> information to refer to the correct kernel functions?
>>>
>>> They don't vary the kernels, that's the point. Once you supply a  
>>> table, the table-lookup kernels will be used. See section 6.6 of  
>>> the 3.3 manual. Such an approach isn't useful to you, since you  
>>> want what amounts to a different functional form depending on the  
>>> value of r. This underscores why you should have been describing  
>>> your objective, so that people trying to help you don't have to  
>>> make shots in the dark - or ignore you until you ask a "right"  
>>> question :-).
>>>
>>> Mark
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>>>
>>
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>
>
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> 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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