On 9/12/13 6:37 PM, Dwey Kauffman wrote:
I carried out independent NPT processes with different tau_p values =
1.5,
1.0 and 0.5
## tau_p 1.5
Energy Average Err.Est. RMSD Tot-Drift
-----------------------------------------------------------------------
--------
Pressure 2.62859 2.6 185.68 2.67572
(bar)
## tau_p 1.0
Energy Average Err.Est. RMSD Tot-Drift
-----------------------------------------------------------------------
--------
Pressure 0.886769 1.7 187.737 0.739
(bar)
## tau_p 0.5
Energy Average Err.Est. RMSD Tot-Drift
-----------------------------------------------------------------------
--------
Pressure 2.39911 2.2 185.708 6.8189
(bar)
##############################
It is clear that when tau_p =1.0, average pressure of the system
(=0.89
bar) is close to ref_p =1.0 bar
However, it is unclear to me as to how to assign a good value to tau_p
in
order to reach at a close value of ref_p. As shown above, both of the
average pressures as tau_p =1.5 and 0.5 are much higher than that as
tau_p
=1.0. A smaller tau_p may or may not help.
As has been mentioned a number of times 0.9 +- 190 and 2.3 +- 190 are not
statistically different. If you use that in a publication then any
conclusions based on that will be rejected.
Statistically, I understood the indistinguishable difference between the
resulted average pressures. Here, I altered tau_p values to determine if
tau_p helps stabilize a desired value of average pressure.
To demonstrate to yourself how variable the pressure is, the tau_p=1 run,
run the pressure analysis again using g_analyze, but using only the first
half and the last half of the trajectory. You will find that the average
values for both parts of the trajectory are not the same.
Thank you for the suggestion of applying g_analyze to trajectory.
Another issue caused by system pressure is about pbc box size. Since I
use
pressure coupling, the box size is not fixed such that protein moved
away
the center of membrane for a long simulation like 30 ns. Box size
That is not due to the pressure coupling.
The changed box-size is problematic because I see that molecules are split.
During NPT process, the box of dimensions (7.12158 7.14945 9.00000)
changed over time to the end at that of dimensions ( 6.43804 6.46323
8.28666). This is because of pressure coupling. See noted also
http://www.gromacs.org/Documentation/Errors#The_cut-off_length_is_longer_than_half_the_shortest_box_vector_or_longer_than_the_smallest_box_diagonal_element._Increase_the_box_size_or_decrease_rlist
Motion of the protein within the
box is simply due to diffusion etc. Also remember, that you have in
effect
an infinite repeating box in all directions, so the "center" of the box is
arbitrary.
If so, how to make a membrane protein relatively fixed (embedded) in bilayer
wthout escaping away during simulation ? In fact, this membrane has
been embedded in membrane by g_membed. Due to diffusion ?? the protein
moved away from bilayer and escaped toward extracellular space.
Is there a way to fix it
or only allow this protein diffusing in xy plane instead of z direction ?
It sounds like you need more thorough equilibration, likely with some
combination of restraints for a period of time. If the protein drifts out of
the membrane, that suggests that the initial forces were fairly high (though not
so high as to cause a crash), thus ejecting the protein from the membrane.
-Justin
If you want the protein to remain in the center for
visualisation purposes, then you do post processing on the box using
trjconv.
Thanks, but this dose not change the fact that protein moved away bilayer
during a long simulation.
changes
significantly during production MD. Is there a way to fix the box size
at
the very beginning ? although turning off pressure coupling will make
box
size fixed.
If you want fixed box dimensions / volume then you perform NVT. But that
will not help with either issues above.
Right. The box of dimensions remains unchanged if pressure coupling is
removed in production MD. However, can it be justified in a system of
membrane protein ? because the purpose of pressure coupling is to
stabilize the pressure and density. For example, for 10 ns simulation, the
average pressure of this system is -5.55 bar, which is less convincing.
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Pressure -5.55572 2.6 155.552 0.846162 (bar)
Thanks.
Dwey
The problem here is you are trying to make comparisons in the behaviour of
simulations where there will not be a statistically significant difference
in the property you are adjusting. Any differences you observe are more
than likely going to be due to chance, rather than pressure.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
[hidden email]
+61 3 9903 9304
---------------------------------
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nail.
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