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

[MD]

Hi,
Yes I am comparing the trajectories side by side and I ran a RMSD of wild
type too.
I looked at the RMSD of wild type and it looks like it became unstable
after 70ns. In this case the only approach is to compare the trajectories
in time windows before 70ns. Would that be right?
Thank you,
MD


On Wed, Apr 11, 2018 at 9:42 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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 <jalemkul at 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
>>>
>>> --
>>> ==================================================
>>>
>>> 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
>>> http://www.thelemkullab.com
>>>
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>>>
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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
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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> Gromacs Users mailing list
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