GROMACS version: 2020.4
GROMACS modification: Yes/No
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Hi. I am simulating a polypropylene melt with MARTINI. I am interested in extracting the bond distribution.
How can I do that? I have found out that maybe “gmx distance” can be used. Though I am a little bit confused with creating a proper index file that includes all the bonds.
Thank you in advance.
HI,
Yes, you have to create an index file with all the pairs for which you want the distance is calculated. you can extract it from the topol file, where all the bonds pairs are already defined.
Of course to calculate the bond distribution makes sense only if you do not run a simulation with bond contraints
Best regards
Alessandra
Hi.
Thanks for your answer.
How can I extract it from the topol file? Do you mean just to copy-paste the pairs? If that’s so, the pairs in the topol file are for a single chain and I want the bonds for all the chains.
Hi,
Sorry I am confuse, do you mean bond or distance?
If you want to calculate the distance between a pair of atoms that are not bonded, you have to generate all the pairs manually.
In case you are not interested in all the distances but in min or max distance may be gmx mindist can help.
Best regards
Alessandra
Hi, Sorry for the confusion.
I mean bonds. I want just to calculate the bond length distribution.