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

[Justin Lemkul]

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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-- 
==================================================

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

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