Dear GROMACS users,
I have a system of 64 chains and want to calculate averaged values of end-to-end distance of all chains as well as the averaged radius of gyration from 1ns trajectory. In the case of end-to-end distance I have prepared index file containing one group of the first atoms in ascending order and the second one containing the terminal atoms in ascending order. I have used g_dist but it looks like it combined all pairs between both groups. I have looked at the mailing list but did not find the answer.
Is it possible to do such analysis using directly GROMACS tools or I need to prepare some scripts with loops running over all chains. Thank you for response in advance.
Zuzana Benkova
I have a system of 64 chains and want to calculate averaged values of end-to-end distance of all chains as well as the averaged radius of gyration from 1ns trajectory. In the case of end-to-end distance I have prepared index file containing one group of the first atoms in ascending order and the second one containing the terminal atoms in ascending order. I have used g_dist but it looks like it combined all pairs between both groups. I have looked at the mailing list but did not find the answer.
Is it possible to do such analysis using directly GROMACS tools or I need to prepare some scripts with loops running over all chains. Thank you for response in advance.
Zuzana Benkova
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