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 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

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Virginia Tech Department of Biochemistry

303 Engel Hall
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Blacksburg, VA 24061

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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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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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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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