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 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 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!

* 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!

* 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.

Reply via email to