I want to calculate the MSID for a polymer melt woth gmx polystat. The manual directs to use the flag -i but I cannot find any other information on it. I have tried with an index file of every atom in the system but am getting a graph I can’t make any sense of even though by other metrics my melt appears equilibrated properly; so I’d like to check I’ve done it right. Should my index file be ordered in a particular way i.e. as is done if you calculate the end to end distance, or can it be in any order?
Hi,
Note I did not use my self the tool.
My understanding is that the index file should include all the polymers atoms. Then tool will calculate the end-of-end distance of each molecule included in the index file.
Did you already try this?
\Alessandra
I am not looking to calculate the end to end distance, but the mean square internal distance (MSID). My point mentioning the end to end distance was to ask if I needed a special order of atoms in my index file, like you need if you want to calculate end to end distance i.e. first and last index of every chain should be the ones you want to calculate the end to end between.
I wrote gmx polystat, but I don’t recall adding the -i option. Someone else must have added that. As an index group you need to supply a list of atom indices of beads, in order along the chains. The internal distances will be computed between those beads.