[gmx-users] Simulation in NPgT ensemble

[Own 12121325]

a question - If I add a negative pressure in xy for the membrane
stretching, using an approach:

pcoupltype = semiisotropic
tau_p 1 1
compressibility 4.5e-5 4.5e-5
ref_p -100 1

will it also increase the diffusion of the solvent along the xy plane of
the membrane, thus mimicking effect of the flow?
Or for that case I need to switch to full anisotropic pressure coupling,
introducing a negative pressure along one selected direction ( e.g along x
or y)?

thanks!

2017-09-26 12:37 GMT+02:00 Own 12121325 <own12121325 at gmail.com>:

> So the question - what the difference will be between A and B and what
> method is better for the lipid bilayer?
>
> (A)
> pcoupltype = semiisotropic
> tau_p 1 1
> compressibility 4.5e-5 4.5e-5
> ref_p -100 1
>
> if the system size in the z-direction is ~ 10nm, then
> this should give a surface tension of (Pz-Plat)*Lz ==
> (1+100)bar*10 nm ~ 10^3 bar nm = 10^3*10^5 N/m2 *10^-9
> m
> =100mN/m assuming the z-dimension Lz remains
> approximately 10 nm throughout the window of
> calculation.
>
>
> (B)
> pcoupltype = surface-tension
> tau_p 1 1
> compressibility 4.5e-5 0 ; Z is fixed
> ref_p -1000 1 ; -1000 is actual surface tension which is the compression
> for the membrane along xy.
>
> 2017-09-25 17:29 GMT+02:00 Own 12121325 <own12121325 at gmail.com>:
>
>> Thanks, Andre!
>>
>> but I have found a lot of peppers, where people have applied constant
>> surface tension simulation using Semi-isotropic coupling. Assuming that the
>> stretching of the membrane is produced via difference in the ref_p along z
>> and xy directions, does the pcoupltype=surface-tension mandatory for such
>> simulations ? Should the xy compressibility be switched to zero assuming
>> that I am interesting in the modeling of stretching of the membrane?
>>
>> 2017-09-25 17:15 GMT+02:00 André Farias de Moura <moura at ufscar.br>:
>>
>>> it is quite well explained in the manual, pcoupltype=surface-tension
>>> Andre
>>>
>>> On Mon, Sep 25, 2017 at 5:38 AM, Own 12121325 <own12121325 at gmail.com>
>>> wrote:
>>>
>>> > Dear Gromacs users!
>>> >
>>> > I wonder to ask whether is possible to perform simulations in NPgT
>>> ensemble
>>> > with the explicit definition of the surface tension value. My system is
>>> > composed of the lipid bilayer solvated in water.
>>> >
>>> > I have found that switching compressibility along x-y to zero and
>>> > introducing bigger negative ref_p along this direction will produce
>>> lateral
>>> > tension on the bilayer according to
>>> >
>>> > g =b*(Pz – Py), where b - is the averaged height of the simulation box
>>> >
>>> >
>>> > I wonder to ask if it also can be realized instead via introduction of
>>> some
>>> > gamma_tension constant as a scaling factor ?
>>> >
>>> >
>>> > Thanks you!
>>> >
>>> >
>>> > Gleb
>>> > --
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>>>
>>>
>>> --
>>> _____________
>>>
>>> Prof. Dr. André Farias de Moura
>>> Department of Chemistry
>>> Federal University of São Carlos
>>> São Carlos - Brazil
>>> phone: +55-16-3351-8090
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>>
>>
>>
>