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

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.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
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> Blacksburg, VA 24061
>
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>
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>
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