The reason why csg_stat and g_rdf work differently can be found here:
<https://groups.google.com/d/msg/votca/UubXtM0GKvc/TDzTG2LNfbkJ>
In short, when you use csg_stat with a mapping (even if it is a 1:1
map) nrexcl get wiped out. This is due to the fact that a mapping
creates a new (exclusion free) topology.
After the mapping VOTCA adds back exclusions for all beads, which are
part of a bonded interaction defined in the mapping file.
In contract when using csg_stat without a mapping file, exclusions are
read from the tpr file.
So to get the same exclusions with and without a mapping you need to
add an extra block with excluded pair to the mapping file.
Compare the output of:
csg_dump --top topol.tpr --excl --cg "PAMcg.xml;watercg.xml"
vs.
csg_dump --top topol.tpr --excl
In your case you need to add:
--- PAMcg.xml.orig 2016-02-16 15:32:09.000000000 -0700
+++ PAMcg.xml 2016-02-16 15:49:19.000000000 -0700
@@ -531,6 +531,39 @@
B29 A29 B30 A30
</beads>
</dihedral>
+ <bond>
+ <name>exclusion</name>
+ <beads>
+ A1 B3
+ A2 B4
+ A3 B5
+ A4 B6
+ A5 B7
+ A6 B8
+ A7 B9
+ A8 B10
+ A9 B11
+ A10 B12
+ A11 B13
+ A12 B14
+ A13 B15
+ A14 B16
+ A15 B17
+ A16 B18
+ A17 B19
+ A18 B20
+ A19 B21
+ A20 B22
+ A21 B23
+ A22 B24
+ A23 B25
+ A24 B26
+ A25 B27
+ A26 B28
+ A27 B29
+ A28 B30
+ </beads>
+ </bond>
</cg_bonded>
</topology>
<maps>
Christoph
2016-02-15 23:11 GMT-07:00 Pallavi Banerjee
<[email protected]>:
> Sure, I am sending all the relevant files.
>
> The interactions A-W, B-W, and W-W are provided as standard input. The
> non-bonded rdfs, A-A.dist.tgt, B-B.dist.tgt, A-B.dist.tgt are generated
> using g_rdf. On performing IBI, if you look at any step, the rdfs coming
> from g_rdf and csg_stat are different. Does csg_stat not take the same
> number of exclusions as does g_rdf?
>
> Thanks in advance!
>
> Kind regards.
> 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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