normal polyelectrolyte gmx distance failing

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3 years 10 months ago #8560 by mboy@seas.upenn.edu
polyelectrolyte gmx distance failing was created by mboy@seas.upenn.edu
Hello!

I am attempting to coarse grain single PMETAC chain in SPC water solution from a recently published atomistic model ( pubs.acs.org/doi/10.1021/acs.langmuir.8b04268 ). I have run a 1 us simulation, and I've attempted to follow the steps listed in the PEO polymer tutorial to get bonded, angle and dihedral distributions. However, when I attempt to calculate the bond length between SC1 (COM of 3 carbon units) along the backbone using the gmx distance function, I am getting segmentation faults.

Has anyone seen this before? Is there some setting in the gmx distance function can change to address this?

Thanks!
Mike

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3 years 10 months ago #8561 by vainikka
Replied by vainikka on topic polyelectrolyte gmx distance failing
Hi,

Are you using the most recent version of GROMACS? If yes, have you checked the GROMACS mailing list?

In case you can't get gmx distance to work, you could just write a short script to compute the COM and distance using something like MDAnalysis.

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3 years 10 months ago #8562 by mboy@seas.upenn.edu
Replied by mboy@seas.upenn.edu on topic polyelectrolyte gmx distance failing
Hi,

thanks for the fast reply. Yes, I'm using gromacs 2020.2. I did some searching but haven't seen anything on the gromacs mailing list.

I'll check out MDAnalysis!

Thanks,
Mike

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