Hi Justin,
Another quick question. When we talk about more independent runs, did you
mean a run with another force field or just simply repeating the run?
Thanks,
Ming

On Wed, Apr 11, 2018 at 10:52 AM, MD <refm...@gmail.com> wrote:

> 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
>>>>>>>>>>>>
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>>>>>>>>>>>> -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
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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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>>>> * Please search the archive at http://www.gromacs.org/Support
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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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