Thank you.
Ming

On Wed, Apr 11, 2018 at 10:46 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 4/11/18 10:44 AM, MD wrote:
>
>> Thank you Justin :)
>> I wonder what is your strategy when considering what criteria could be
>> used
>> for determining convergence of the simulation?
>>
>
> If all the relevant quantities that I care about are invariant over time
> based on error estimates, it's converged.
>
> -Justin
>
>
> Ming
>>
>> On Wed, Apr 11, 2018 at 10:30 AM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>> On 4/11/18 10:26 AM, MD wrote:
>>>
>>> Thank you Justin. Two quick questions (learning questions :))
>>>> 1. How do I apply several invocations of trjconv, (a quick guide would
>>>> be
>>>> appreciated)
>>>>
>>>> http://www.gromacs.org/Documentation/Terminology/Periodic_
>>> Boundary_Conditions#Suggested_trjconv_workflow
>>>
>>> If I had $0.10 for every time I posted that link, I could fund my summer
>>> salary... :)
>>>
>>> 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?
>>>>
>>>> Whenever a given time frame has been chosen for a particular analysis,
>>> it
>>> should be accompanied by an explanation of why that time frame was
>>> chosen.
>>> Is it because the authors believed the simulation did not converge until
>>> 90
>>> ns, and therefore they discarded 0-90 ns and only analyzed from 90-100
>>> ns?
>>> That may be the case, but for a slow-converging system, I would expect
>>> the
>>> simulation to be run much longer to collect more data. 10 ns is not much
>>> time at all for anything useful.
>>>
>>> RMSF is particularly sensitive to equilibration; the initial frames in
>>> unrestrained MD are often not valid to include in this analysis, but one
>>> should consider very carefully what criteria are being used for
>>> determining
>>> convergence of the simulation. No one quantity will tell you this, even
>>> if
>>> it is aesthetically pleasing.
>>>
>>> -Justin
>>>
>>> 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 simulatio
>>>>>>>>>>>> <https://maps.google.com/?q=is+mean+that+I+should+trust+the+simulatio&entry=gmail&source=g>n
>>>>>>>>>>>> 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
>>>>>>>>>>>
>>>>>>>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>>>>>>>> /Mailing_Lists/GMX-Users_List before pos
>>>>>>>>>>> <https://maps.google.com/?q=/Mailing_Lists/GMX-Users_List+be
>>>>>>>>>>> fore+pos&entry=gmail&source=g>
>>>>>>>>>>>
>>>>>>>>>>> ting!
>>>>>>>>>>>
>>>>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>>>>
>>>>>>>>>>> * For (un)subscribe requests visit
>>>>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx
>>>>>>>>>>> -users
>>>>>>>>>>> or
>>>>>>>>>>> send a mail to gmx-users-requ...@gromacs.org.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>>
>>>>>>>>>>> ==================================================
>>>>>>>>>>>
>>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>>>>>
>>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>>
>>>>>>>>> * For (un)subscribe requests visit
>>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>>>>> or
>>>>>>>>> send a mail to gmx-users-requ...@gromacs.org.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>>
>>>>>>>> ==================================================
>>>>>>>
>>>>>>> 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
>>>>>>>
>>>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>>>
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>>>>>>> or
>>>>>>> send a mail to gmx-users-requ...@gromacs.org.
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>> ==================================================
>>>>>
>>>>> 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
>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>> /Mailing_Lists/GMX-Users_List before posting!
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>>>>> send a mail to gmx-users-requ...@gromacs.org.
>>>>>
>>>>>
>>>>> --
>>> ==================================================
>>>
>>> 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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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==================================================
>
> 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
>
> * Please search the archive at http://www.gromacs.org/Support
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