# [gmx-users] RE: average pressure of a system

Dwey Kauffman mpi566 at gmail.com
Fri Sep 13 00:37:01 CEST 2013

```>> 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 ?

> 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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