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

[MD]

Hi,

I wouldn't do cherry-picking. I am just confused how I can trust the data
if the RMSD goes crazy in that range? Also based on the command I used I
think the PBC has been taken care of, please correct me if I am wrong :)

And It would be very interesting, if the RMSF of wild type started
fluctuating after 70 ns for real.

Also, yes you are right, this is a single run and I will need to replicate
the simulation for several times. At the mean time I  would really like to
learn how I can make a judgement which ranges of data I could use for the
analysis :)

Thank you,

MD

On Wed, Apr 11, 2018 at 10:08 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>>>>
>>>>> ==================================================
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>
>>> ==================================================
>>>
>>> --
>>> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
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