[votca] Re: Reading exclusions

[Pallavi Banerjee]

Thank you, Christoph! 

Also, there seems to be a discrepancy in the calculation of rdfs between 
csg_stat and g_rdf. The rdfs obtained from both are different, even on 
using the same tpr file as input. 

I am performing iterations over both bonded and non-bonded interactions, 
with two types of beads, A and B in my system. Bonded interactions are the 
following: bond AB, angle ABA, angle BAB, dihedral BABA. Non-bonded are 
A-A, B-B, and A-B. The difference is seen with just the interaction A-B. I 
am attaching the rdfs from csg_stat and g_rdf. Could anyone provide the 
code by which csg_stat calculates rdf ? What could be going wrong here?

Thanks in advance!

-Pallavi Banerjee

On Sunday, February 14, 2016 at 5:05:59 PM UTC+5:30, Pallavi Banerjee wrote:
>
> Hello users,
>
> I am not sure as to how I should interpret the list of exclusions that 
> csg_dump generates. I have a polymer of 60 beads. I use number of 
> exclusions as 3 in my topology file. The following is what csg_dump spits 
> out:
>
> 1 2 3 4 6
> 2 3 4
> 3 4 5 6 8
> 4 5 6
> 5 6 7 8 10
> 6 7 8
> 7 8 9 10 12
> 8 9 10
> 9 10 11 12 14
> 10 11 12
> 11 12 13 14 16
> 12 13 14
> 13 14 15 16
> 18 13 15 16 17 19 20
> 14 15 16
> 15 16 17 20
> 16 17
> 17 19 20 22
> 19 20 21 22 24
> 20 21 22
> 21 22 23 24 26
> 22 23 24
> 23 24 25 26 28
> 24 25 26
> 25 26 27 28 30
> 26 27 28
> 27 28 29 30 32
> 28 29 30
> 29 30 31 32
> 34 29 31 32 33 35 36
> 30 31 32
> 31 32 33 36
> 32 33
> 33 35 36 38
> 35 36 37 38 40
> 36 37 38
> 37 38 39 40 42
> 38 39 40
> 39 40 41 42 44
> 40 41 42
> 41 42 43 44 46
> 42 43 44
> 43 44 45 46 48
> 44 45 46
> 45 46 47 48 50
> 46 47 48
> 47 48 49 50 52
> 48 49 50
> 49 50 51 52 54
> 50 51 52
> 51 52 53 54 56
> 52 53 54
> 53 54 55 56 58
> 54 55 56
> 55 56 57 58 60
> 56 57 58
> 57 58 59 60
> 58 59 60
> 59 60
>
>
> I don't understand why there are 5/6 beads in one row, when my number of 
> exclusions is only 3. 
>
> Thanks in advance!
>
> -Pallavi Banerjee
>

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rdf_A_A.xvg
Description: Binary data

rdf_B_B.xvg
Description: Binary data

rdf_A_B.xvg
Description: Binary data