[gmx-users] Simulation in NPgT ensemble
own12121325 at gmail.com
Tue Sep 26 12:37:27 CEST 2017
So the question - what the difference will be between A and B and what
method is better for the lipid bilayer?
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
=100mN/m assuming the z-dimension Lz remains
approximately 10 nm throughout the window of
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
>> On Mon, Sep 25, 2017 at 5:38 AM, Own 12121325 <own12121325 at gmail.com>
>> > Dear Gromacs users!
>> > I wonder to ask whether is possible to perform simulations in NPgT
>> > 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
>> > 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
>> > 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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