Hi ALL, Its a very basic question but still... When we calculate RMSD (or any other parameter) using the g_rms command, we need to supply the .tpr file with -s option. Now suppose if I have a total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will be 4 .tpr files. So at the end of 20 ns if I wish to calculate RMSD, then which .tpr file should I suppy to g_rms, the first one or the last one? We I run g_rms with the two .tpr files, I get different results. So which one should be used? Any suggestion is welcome.
Thanks, Anirban
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