GROMACS version: 2020.4
GROMACS modification: No
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I wanted to calculate properties such as end-to-end distance and radius of gyration of a branched polymer. So I created an index file for the polymer making sure the first and last indices constitute the ends of the longest chain. E.g.,
[ mol1 ]
10 1 2 3 4 5 6 8 9 11 … 42 7
When I tried to use the same index file to calculate msd, I got an error,
Calculating diffusion coefficients for molecules.
Reading file md_1.tpr, VERSION 2020.4 (single precision)
Reading file md_1.tpr, VERSION 2020.4 (single precision)
Select a group to calculate mean squared displacement for:
Group 0 ( mol) has 42 elements
There is one group in the index
Program: gmx msd, version 2020.4
Source file: src/gromacs/gmxana/gmx_msd.cpp (line 888)
Fatal error:
The index group does not consist of whole molecules
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
I noticed the error goes away if I use an index file where the atoms are numbered in order.
I wanted to report this issue so that it might be solved in future versions (if already not solved). I do understand that indices of the same molecule should be together in the case the where the group contains multiple molecules. I just do not understand why the indices in the molecule has to ordered in a certain way. Please let me know if I am not considering something.
Thank you in advance.