csg_boltzmann list does not list all available interactions

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nancyfor

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Dec 26, 2020, 6:29:57 PM12/26/20
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Hello everybody,

I am trying to get the probability distribution functions and the tabulated potentials  for a system with 11 coarse grained beads. However when listing all available bonded interaction only list 3.  Coincidentally, they are the last bonded interactions for angle, bond and dihedral sections respectively. I am using votca 1.6.2 and gromacs 2019.4

This is the output for 

csg_boltzmann --top topol.tpr --trj traj.xtc --cg mapping.xml
list 

Available bonded interactions:
molecule 0:EMBT:index 0
molecule 0:MBT:index 0
molecule 0:SMEMBT:index 0

I have checked if the mapping was correct using csg_dump, and it seems is fine.

I have attached the mapping file in case you spot any mistake.
Best regards, 
Nancy 

mapping.xml

Christoph Junghans

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Dec 26, 2020, 7:23:11 PM12/26/20
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Yeah, you need to put each bond, angle, dihedral in its own <bond>,
<angle>, <dihedral> block, otherwise all properties (name, beads etc)
will be overwritten by the latest entry and hence you end up with one
of each.

If the documentation is unclear on that, please modify the
input_files.rst file in the share/doc folder of the csg module and
send up as a patch or submit a pull request on GitHub.

Christoph

> Best regards,
> Nancy
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nancyfor

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Dec 27, 2020, 4:18:45 AM12/27/20
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Thanks Christoph, I completely overlooked this. 
Cheers, 
Nancy

nancyfor

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Dec 27, 2020, 6:56:05 AM12/27/20
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Hi Christoph,

I have corrected the mapping file. However, when creating the exclusion.txt I noticed this file was not correct. For this I generated a .tpr file without exclusions
and use:

csg_boltzmann --top mma_trimer_sd_noexclusions.tpr --cg mma_trimer_mapping.xml --excl exclusions.txt

I used votca 1.6.2.  I tried two other versions of votca, sourcing someone else installation, votca 1.6-dev and a local machine version.

I supposed this is a problem with my installation. Is there a way to check that votca was installed correctly? I did not get any error while installing it. And I have not seen anyone with this problem browsing the messages. 

I have attached the mapping file and the exclusion files for the different votca versions. 

details of the versions below

csg_boltzmann, version 1.6.2 gitid: 9b6bbd0 (compiled Dec 19 2020, 15:56:40)
votca_tools, version 1.6.2 gitid: 9b6bbd0 (compiled Dec 19 2020, 15:55:42)
gromacs, 2019.4 (single precision)


csg_boltzmann, version 1.6-dev gitid: e42c3e100 (compiled Jun 30 2020, 17:41:20)
votca_tools, version 1.6-dev gitid: e42c3e100 (compiled Jun 30 2020, 17:40:52)
gromacs, 2019.4 (single precision)


csg_boltzmann, version 1.5  (compiled Feb  8 2019, 02:59:36)
votca_tools, version 1.5  (compiled Feb  8 2019, 02:57:53)
gromacs, 2019.1 (double precision)
mma_trimer_mapping.xml
exclusions_csgv1.6.2.txt

nancyfor

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Dec 27, 2020, 7:01:55 AM12/27/20
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The rest of the files: 

I have also check the exclusions with the csg_dump, again with the different versions. Using 

csg_dumpp --top mma_trimer_sd_noexclusions.tpr  --excl

I got the same output for the three cases. 

Not sure what is happening.
Cheers
Nancy
exclusions_csgv1.6-dev.txt
exclusions_csgv1.5.txt
check_exclusions_csgv1.6.2.txt

Christoph Junghans

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Dec 27, 2020, 12:01:09 PM12/27/20
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Can you send the tpr file as well?

nancyfor

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Dec 27, 2020, 12:20:51 PM12/27/20
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Here is the file 

mma.tar.gz

Christoph Junghans

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Dec 27, 2020, 3:38:44 PM12/27/20
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Thanks I will have a look at it in the next few days and get back to you!

Just to clarify, csg_dump and csg_boltzmann are not printing the same exclusions.
csg_dump prints the exclusions read for the topology file when used without a mapping, and the exclusions generated by the coarse-grained bonded interaction when used with a mapping file. The former is gone in atomistic atom numbering, while the latter is done in coarse-grained atomic numbering.
While csg_boltzmann prints the exclusions in atomistic numbering generated by the bonded interactions from the mapping to coarse-grained beads.

Christoph

On Sun, Dec 27, 2020 at 10:20 nancyfor <nanc...@gmail.com> wrote:
Here is the file 


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Christoph Junghans

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Dec 27, 2020, 6:05:58 PM12/27/20
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Could you also send the sources (gro, top [and custom includes] & mdp)
to make the tpr, I want to run it with an older version of gromacs,
too.

Christoph

On Sun, Dec 27, 2020 at 10:20 AM nancyfor <nanc...@gmail.com> wrote:
>
> Here is the file
>
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nancyfor

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Dec 27, 2020, 6:18:14 PM12/27/20
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Hi Christoph
attached are the .gro, .top, .mdp and .xml
Thanks!

files.tar.gz

Christoph Junghans

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Dec 29, 2020, 9:26:55 AM12/29/20
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Ok, it seems somewhere in 1.6 we introduced a bug in the --excl
option, see https://github.com/votca/csg/pull/625.
We hopefully find it soon.

For your system the exclusion should look like this:
# atomistic: 3-MMA cg: 3-MMA cgmap: mapping.xml
1 42 43 44 45
2 42 43 44 45
3 42 43 44 45
4 42 43 44 45
5 42 43 44 45
6 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51
7 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51
8 25 26 27 28 29 30 31 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53
9 25 26 27 28 29 30 31 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53
10 25 26 27 28 29 30 31 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
50 51 52 53
11 25 26 27 28 29 30 31 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
50 51 52 53
12 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51
13 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51
14 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51
15 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51
16 27 28 29 30 40 41 42 43 44 45 46 48 49 50 51
17 42 43 44 45
18 42 43 44 45
19 42 43 44 45
25 42 43 44 45
26 42 43 44 45
27 40 41 42 43 44 45 46 48 49 50 51
28 40 41 42 43 44 45 46 48 49 50 51
29 40 41 42 43 44 45 46 48 49 50 51
30 40 41 42 43 44 45 46 48 49 50 51
31 42 43 44 45

Christoph
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nancyfor

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Dec 29, 2020, 9:52:50 AM12/29/20
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Thanks Christoph! 

Christoph Junghans

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Jan 9, 2021, 6:30:56 PM1/9/21
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This bug is now fixed in the stable branch, we will make another 1.6 release soon that includes the fix, too!

Christoph 

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