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

Justin Lemkul jalemkul at vt.edu
Wed Apr 11 15:24:14 CEST 2018

On 4/11/18 9:22 AM, MD 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.

It sounds to me like one simulation isn't properly corrected for PBC 
effects (protein jumping back and forth) while the other is. Make sure 
the trajectory is sensible; gmx rmsf doesn't intrinsically account for 
PBC so you have to judiciously apply trjconv before running the analysis.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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