[gmx-users] RMSF started increasing after 60 ns simulation

MD refmac5 at gmail.com
Wed Apr 11 15:22:10 CEST 2018

Hi Gromacs folks,

I was trying to use RMSF to compare c-alpha of a wild type and mutant in a
100 ns simulation. I discarded the 10-30 ns and compared them side by side
in non-overlapping time windows of 30-40ns, 40-50ns, 50-60ns, 60-70 ns,
70-80 ns, 80-90 ns and 90-100ns. The RMSF of wild type and mutant overlay
pretty well with exceptions of some regions with minor flexibility
differences, but the c-alpha RMSF of wild type went crazy starting from
70-80ns (7-8 folds of a more drastic change) and lasted until the end,
while the mutant stayed in the same range of changing.

Does this mean that I should trust the simulation after 70ns, or I should
continue the simulation and see if the system will calm down eventually?
Any help will be appreciated.



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