On 4/11/18 9:41 AM, MD wrote:
Hi Justin,

This was the command I used for both wild type and mutant. I wonder if you
could think of any reason that made only the wild type have the PBC
effects?

gmx trjconv -s md.tpr -f md.xtc -o md_noPBC.xtc -pbc mol -ur compact

Visualize each trajectory as Mark suggested.

-Justin

Thank you,

MD

On Wed, Apr 11, 2018 at 9:23 AM, Justin Lemkul <jalem...@vt.edu> wrote:


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

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==================================================

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

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

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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