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

Mark Abraham mark.j.abraham at gmail.com
Wed Apr 11 15:23:27 CEST 2018


What did you learn from viewing the trajectory in a visualization tool?


On Wed, Apr 11, 2018 at 3:22 PM MD <refmac5 at gmail.com> wrote:

> 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.
> Thanks,
> MD
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