segmentation error in csg_stat
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Pratyasha Bhardwaj
Mar 27, 2024, 7:29:22 AMMar 27
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Dear Users,
I have been trying to obtain the rdfs for my system. however, I get segmentation fault:
begin to calculate distribution functions
# of bonded interactions: 0
# of non-bonded interactions: 10
Segmentation fault
begin to calculate distribution functions
# of bonded interactions: 0
# of non-bonded interactions: 10
Segmentation fault
1. I have a doubt about the minimum and maximum values to be entered in the settings file. How do I decide on that?
2. My system has 2 different molecules and 4 different atom types. My mapping scheme is almost 1 Kuhn segment representing 1 CG bead. Thus, for a polyethylene molecule, 1 CG bead will represent about 5 ethylene monomers. Is it incorrect to use such high level coarse graining if I want to use IBI
3. I was able to obtain the bond and angle potentials using csg_boltzmann. However, the error comes when I use csg_stat. Where am i going wrong? What does this error mean?
3. I was able to obtain the bond and angle potentials using csg_boltzmann. However, the error comes when I use csg_stat. Where am i going wrong? What does this error mean?
I am attaching my files here. The trajectory,gro file and tpr file can be found using this link: https://drive.google.com/drive/u/0/folders/10MOUsNZqZctHYm8ithO7wndp1rzaQiAe
Any help will be really appreciated.
Any help will be really appreciated.
Thank you
Sincerely,
Pratyasha
Christoph Junghans
Mar 30, 2024, 10:02:42 AMMar 30
to vo...@googlegroups.com
On Wed, Mar 27, 2024 at 5:29 AM Pratyasha Bhardwaj
<pratya...@gmail.com> wrote:
>
> Dear Users,
>
> I have been trying to obtain the rdfs for my system. however, I get segmentation fault:
> begin to calculate distribution functions
> # of bonded interactions: 0
> # of non-bonded interactions: 10
> Segmentation fault
>
> 1. I have a doubt about the minimum and maximum values to be entered in the settings file. How do I decide on that?
> 2. My system has 2 different molecules and 4 different atom types. My mapping scheme is almost 1 Kuhn segment representing 1 CG bead. Thus, for a polyethylene molecule, 1 CG bead will represent about 5 ethylene monomers. Is it incorrect to use such high level coarse graining if I want to use IBI
> 3. I was able to obtain the bond and angle potentials using csg_boltzmann. However, the error comes when I use csg_stat. Where am i going wrong? What does this error mean?
In your settings file you are reusing the name "POL-POL" 6x, but
<pratya...@gmail.com> wrote:
>
> Dear Users,
>
> I have been trying to obtain the rdfs for my system. however, I get segmentation fault:
> begin to calculate distribution functions
> # of bonded interactions: 0
> # of non-bonded interactions: 10
> Segmentation fault
>
> 1. I have a doubt about the minimum and maximum values to be entered in the settings file. How do I decide on that?
> 2. My system has 2 different molecules and 4 different atom types. My mapping scheme is almost 1 Kuhn segment representing 1 CG bead. Thus, for a polyethylene molecule, 1 CG bead will represent about 5 ethylene monomers. Is it incorrect to use such high level coarse graining if I want to use IBI
> 3. I was able to obtain the bond and angle potentials using csg_boltzmann. However, the error comes when I use csg_stat. Where am i going wrong? What does this error mean?
interaction names need to be unique. That might cause the segfault.
Christoph
>
> I am attaching my files here. The trajectory,gro file and tpr file can be found using this link: https://drive.google.com/drive/u/0/folders/10MOUsNZqZctHYm8ithO7wndp1rzaQiAe
> Any help will be really appreciated.
>
> Thank you
> Sincerely,
> Pratyasha
>
> --
> I am attaching my files here. The trajectory,gro file and tpr file can be found using this link: https://drive.google.com/drive/u/0/folders/10MOUsNZqZctHYm8ithO7wndp1rzaQiAe
> Any help will be really appreciated.
>
> Thank you
> Sincerely,
> Pratyasha
>
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Christoph Junghans
Web: http://www.compphys.de
Pratyasha Bhardwaj
Mar 31, 2024, 7:07:57 AMMar 31
to vo...@googlegroups.com
Dear Christoph,
Thank you for pointing that out. What about setting the minimum and maximum distance. Do we set the maximum in the settings file for rdf calculation according to the force cutoff we used in the all-atomistic simulation?
Sincerely,
Pratyasha
Thank you for pointing that out. What about setting the minimum and maximum distance. Do we set the maximum in the settings file for rdf calculation according to the force cutoff we used in the all-atomistic simulation?
Sincerely,
Pratyasha
To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e7xbfW7R3uLBNXAkicVY244vHzGV8s%2BKvdxrDA%3DCoZMuQ%40mail.gmail.com.
Christoph Junghans
Mar 31, 2024, 6:32:53 PMMar 31
to vo...@googlegroups.com
I don't think the min and max matter much at this stage, you will just
get a lot of zeros in the histogram. Once you start IBI you will have
to set them more carefully.
Christoph
On Sun, Mar 31, 2024 at 5:07 AM Pratyasha Bhardwaj
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAOq_SnV4ocWe9PWuJPg9h2zeAiWDbR9oaUSgNgpzFGtd87xnLw%40mail.gmail.com.
get a lot of zeros in the histogram. Once you start IBI you will have
to set them more carefully.
Christoph
On Sun, Mar 31, 2024 at 5:07 AM Pratyasha Bhardwaj
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