[gmx-users] Membrane: anisotropic pressure coupling

[Justin A. Lemkul]

Rebeca García Fandiño wrote:
> Hello,
> 
> I am new in Gromacs, and I am trying to simulate the interaction between 
> a DOPC membrane and a protein.
> 
> I have equilibrated my system at constant volume and now I would like to 
> switch to constant pressure.
> 
> I think the best option for me is to use ANISOTROPIC pressure, because I 
> want to study the ondulations produced in the membrane due to the 
> protein. Do you recommend anisotropic pressure for this? or 
> semiisotropic would be enough?

A good discussion of such topics can be found in: Kandt, et al. (2007) Methods 
41: 475-488.

> 
> Another question is about the values of tau_p and ref_p. I have read in 
> the manual that in the case of anisotropic pressure I should use 6 
> values. Which values do you recommend to use? Should I use also 6 values 
> for compressibility and ref_p?
> 
>  
> 
> Pcoupl      = Berendsen
> 
> Pcoupltype  = anisotropic
> 
> tau_p       =  2.0 2.0  2.0  2.0  2.0  2.0        
> 

Only one value of tau_p is necessary.

> compressibility  =  4.5e-5 4.5e-5 4.5e-5  4.5e-5 4.5e-5    4.5e-5
> 

Setting the off-diagonal compressibilities as such may lead to deformations of 
the box.  From the manual:

"When the off-diagonal compressibilities are set to zero, a rectangular box will 
stay rectangular. Beware that anisotropic scaling can lead to extreme 
deformation of the simulation box."

> ref_p       =  1.0  1.0  1.0  1.0  1.0  1.0

Similarly, you are specifying a pressure in the diagonal directions (the last 
three values).

-Justin

> 
>  
> 
> Thank you very much for your help in advance.
> 
>  
> 
> Best wishes,
> 
>  
> 
> Rebeca García Fandiño
> 
> Parc Cientific de Barcelona
> 
> regafan at hotmail.com
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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