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

[MD]

Hi Mark,

I found some of the regions are more flexible in the mutant in several time
windows but not in the others. Should I trust the later time windows than
the former ones?

Thanks,

MD

On Wed, Apr 11, 2018 at 9:23 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> What did you learn from viewing the trajectory in a visualization tool?
>
> Mark
>
> 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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