[gmx-users] Simulation in NPgT ensemble

[Own 12121325]

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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