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

[Justin Lemkul]

On 4/11/18 10:04 AM, MD wrote:
> 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?

I'd argue that that's cherry-picking, taking preferable data and 
ignoring the real outcome. If the protein structure goes haywire (and it 
really, truly isn't a PBC effect, which it is in about 9 out of 10 
cases...) then you should investigate what's going on. Maybe the .mdp 
settings are incorrect and causing the model physics to break down. 
Maybe the force field you chose is not sufficiently accurate for 
simulating the system. Is the behavior reproducible across multiple 
simulations, or are you looking at an outlier?

-Justin

> 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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>> --
>> ==================================================
>>
>> 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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>
>

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

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

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