[gmx-users] RE: average pressure of a system
Justin Lemkul
jalemkul at vt.edu
Fri Sep 13 04:31:02 CEST 2013
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
>> ---------------------------------
>> When the only tool you own is a hammer, every problem begins to resemble a
>> nail.
>>
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>> NAML
>
>
>
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--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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