Thank you Justin. Two quick questions (learning questions :))
1. How do I apply several invocations of trjconv, (a quick guide would be
appreciated)
2. Several literature used only 90-100 ns time window for RMSF analysis in
a 100ns run. Does that mean the later the time window is the more value of
RMSF it has?
Thanks again,
MD

On Wed, Apr 11, 2018 at 10:17 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 4/11/18 10:16 AM, MD wrote:
>
>> 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 :)
>>
>
> The best tool you have is your eyes. Watch the trajectory. Understand what
> is happening during the time points for which the data behave very
> differently. Maybe something interesting is happening and you need to
> consider it. Maybe your PBC treatment is inadequate (often you need several
> invocations of trjconv to get things right, very few cases allow you to use
> a single, magic command).
>
>
> -Justin
>
> Thank you,
>>
>> MD
>>
>> On Wed, Apr 11, 2018 at 10:08 AM, Justin Lemkul <jalem...@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 <jalem...@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 <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
>>>>>>> <https://maps.google.com/?q=trajectory+is+sensible;+gmx+rmsf+doesn't+&entry=gmail&source=g>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
>>>>>>>
>>>>>>> jalem...@vt.edu | (540) 231-3129
>>>>>>> http://www.thelemkullab.com
>>>>>>>
>>>>>>> ==================================================
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Gromacs Users mailing list
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>>>>>>> * Please search the archive at http://www.gromacs.org/Support
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>>>>>>> <https://maps.google.com/?q=/Mailing_Lists/GMX-Users_List+before+pos&entry=gmail&source=g>
>>>>>>> ting!
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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
>>>>>
>>>>> jalem...@vt.edu | (540) 231-3129
>>>>> http://www.thelemkullab.com
>>>>>
>>>>> ==================================================
>>>>>
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>>>>> Gromacs Users mailing list
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>>>>> * Please search the archive at http://www.gromacs.org/Support
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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
>>>
>>> jalem...@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
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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