Reading exclusions

[Pallavi Banerjee]

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

[Christoph Junghans]

2016-02-14 4:35 GMT-07:00 Pallavi Banerjee
<palla...@students.iiserpune.ac.in>:

That is more a question for the gromacs people, but in short "nrexcl =
3 stands for excluding non-bonded interactions between atoms that are
no further than 3 bonds away." (from the gromacs manual). So if you
have atoms off the side( which are not on the backbone) they will
generate more than 3 exclusions.

Christoph

> Thanks in advance!
>
> -Pallavi Banerjee
>

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[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

[Christoph Junghans]

2016-02-15 5:12 GMT-07:00 Pallavi Banerjee
<palla...@students.iiserpune.ac.in>:

> 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?

I think only attached the xvg file, but not the dist.new files.
However, this is hard to debug from the distributions anyhow, so could
you send the following files to give us more insight:
- settings.xml
- conf.gro
- topol.top (+ non-standard include files)
- grompp.mdp
- index.ndx
to the mailing list or de...@votca.org (if you don't like to share them
here) or open an issue here <https://github.com/votca/csg/issues>.

Christoph

[Pallavi Banerjee]

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:

[Christoph Junghans]

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
<palla...@students.iiserpune.ac.in>:

[Pallavi Banerjee]

Thank you, Christoph! That worked beautifully. All the interactions are well-converged now.

Best regards,

Pallavi Banerjee

On Sunday, February 14, 2016 at 5:05:59 PM UTC+5:30, Pallavi Banerjee wrote: