IBI error: segmentation fault at csg_inverse step of IBI in step001

[Pragati Sharma]

Dear all,

I am trying to run CG simulations of 5mer-polybutadiene using IBI method and following hexane tutorial.

I am getting segmentation fault at step 1, when I run csg_inverse command.

Below are the steps I followed and files attached. Please guide me towards the probable reason of the error.

1. csg_mapp and csg_gmxtopol " generate cg.gro and cg.top

2.Run run_Boltzman.sh script to get target distributions and potentials (This gives tabulated potential  files for bonded interactions only)

3. Run run.sh script (for getting non-bonded potentials): I provide the tabulated bonded potentials obtained in step 2 here for simulation and run csg_inverse. In this step the error comes.

Sometimes the error shows infinite potential energy in the system.

I guess there is some issue with my bonded potentials. I have read you have to "manually delete poorly sampled parts" from potential files. How to do it, If that is the reason.

I am attaching the potential files here.

Thanks

[Christoph Junghans]

Can you have a look in inverse.log to see what is the last command?
(That will most likely be the one that segfaults)

Christoph
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Christoph Junghans
Web: http://www.compphys.de

[Pragati Sharma]

It is the mdrun command, where the error comes. I have attached the inverse.log file here also. Thanks.

[Christoph Junghans]

On Wed, Aug 5, 2020 at 9:04 PM Pragati Sharma <praga...@gmail.com> wrote:
>
>
> It is the mdrun command, where the error comes. I have attached the inverse.log file here also. Thanks.

That usually means your system exploded, maybe there is a message from
mdrun in one of the log files as well.
The reason for that is most likely that one of the bonded interactions
is screwed up.
You could try to run it with harmonic interactions as a start to check that.

Christoph

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[Pragati Sharma]

Thanks Christoph. I can solve the segmentation fault and simulation runs for 1 step, however it does not go to second step and stops with below error:
 
"Topology does not have beads of type "C"
This was specified in type1 of interaction "C-C"

If there is any problem with topology, it should not run the first step also. Is there any issue with the molecule names??? Because it also says a warning: WARNING: unknown molecule "CGBUT" with id 1 in topology
I am attaching the two coarse grained topology files and inverse.log file and mdp file also.

Along with this problem, the tabulated potentials for non-bonded interactions generated in step 1 gives all values as zero. Why is it?? Is it because I am not using exclusions?

Thanks in advance.

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[Pragati Sharma]

Hello all, I solved the topology mismatch issue and my CG simulation is now running.

But I am still struggling to understand the values I got in table_nonbonded entries ike this: 

0.0000000000e+00   0.0000000000e+00 0.0000000000e+00   0.0000000000e+00 0.0000000000e+00   1.3613480400e+04  0.0000000000e+00
2.0000000000e-03   0.0000000000e+00 0.0000000000e+00   0.0000000000e+00 0.0000000000e+00   1.3051740430e+04  2.7608764250e+05
4.0000000000e-03   0.0000000000e+00 0.0000000000e+00   0.0000000000e+00 0.0000000000e+00   1.2509129830e+04  2.6620522750e+05
6.0000000000e-03   0.0000000000e+00 0.0000000000e+00   0.0000000000e+00 0.0000000000e+00   1.1986919520e+04  2.5568735500e+05
8.0000000000e-03   0.0000000000e+00 0.0000000000e+00   0.0000000000e+00 0.0000000000e+00   1.1486380410e+04  2.4453402500e+05
1.0000000000e-02   0.0000000000e+00 0.0000000000e+00   0.0000000000e+00 0.0000000000e+00   1.1008783420e+04  2.3375991250e+05
1.2000000000e-02   0.0000000000e+00 0.0000000000e+00   0.0000000000e+00 0.0000000000e+00   1.0551340760e+04  2.2442411500e+05

There are seven columns, e.g in table_A_A.xvgfile. What are these entries for? Which one represents potential.  

Thanks in advance.

[Christoph Junghans]

On Wed, Aug 19, 2020 at 4:44 AM Pragati Sharma <praga...@gmail.com> wrote:
>
>
> Hello all, I solved the topology mismatch issue and my CG simulation is now running.
> But I am still struggling to understand the values I got in table_nonbonded entries ike this:
>
> 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 1.3613480400e+04 0.0000000000e+00
> 2.0000000000e-03 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 1.3051740430e+04 2.7608764250e+05
> 4.0000000000e-03 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 1.2509129830e+04 2.6620522750e+05
> 6.0000000000e-03 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 1.1986919520e+04 2.5568735500e+05
> 8.0000000000e-03 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 1.1486380410e+04 2.4453402500e+05
> 1.0000000000e-02 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 1.1008783420e+04 2.3375991250e+05
> 1.2000000000e-02 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 0.0000000000e+00 1.0551340760e+04 2.2442411500e+05
> There are seven columns, e.g in table_A_A.xvgfile. What are these entries for? Which one represents potential.

See section 5.8.12 of the gromacs manual:
http://manual.gromacs.org/2019/manual-2019.pdf
In short, VOTCA stores the potentials in a files called <name>.pot.cur
and then converts in to an xvg file for gromacs.
The xvg file has seven columns for x(=distance0, colomb, coulomb
forces,C6, C6 forces C12 and C12 forces.
VOTCA uses the C12 part instead of the C6 or a mixture.

Christoph

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