[gmx-users] exclusions

[Mark Abraham]

On 12/05/2011 2:43 AM, Gavin Melaugh wrote:
> Regarding my earlier post- If someone could confirm.
> Taking into account that atom indices start from zero.
> Then excls[0] = exclusions centred around atom 1.
> [0..12] = there are 13 exclusions each one labelled form 0-12.
> I then assume that you read the exclusions with respect to atom 0
> (actual index =1)

I doubt it. I think each particle excludes itself in the list. Make a 
simple system where you can compute the exclusions by hand and see what 
the data structure is doing. Then vary it until you're happy with your 
deductions.

Mark

> In the next set do you read the exclusion with respect to atom 1 (actual
> index =2).
> and so on ....
>
>
> Many thanks in advance
>
> Gavin
> Gavin Melaugh wrote:
>> Hi all
>>
>> I am cheking the non binary version topol.tpr form grompp and I was
>> wondering what the following format for the exclusion section signifies?
>>
>> excls:
>>           nr=228
>>           nra=1920
>>           excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16}
>>           excls[1][13..25]={0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 15}
>>
>>
>> Also I take it, that this is a result of nrexcl =3
>>
>> Cheers
>>
>> Gavin
>>