Re: [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 :

> 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 :
>
>> 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 :
>>
>>> it is quite well explained in the manual, pcoupltype=surface-tension
>>> Andre
>>>
>>> On Mon, Sep 25, 2017 at 5:38 AM, Own 12121325 
>>> 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
>>> > --
>>> > Gromacs Users mailing list
>>> >
>>> > * Please search the archive at http://www.gromacs.org/
>>> > Support/Mailing_Lists/GMX-Users_List before posting!
>>> >
>>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> >
>>> > * For (un)subscribe requests visit
>>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> > send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
>>>
>>>
>>> --
>>> _
>>>
>>> Prof. Dr. André Farias de Moura
>>> Department of Chemistry
>>> Federal University of São Carlos
>>> São Carlos - Brazil
>>> phone: +55-16-3351-8090
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
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>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>
>>
>>
>
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Re: [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 :

> 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 :
>
>> it is quite well explained in the manual, pcoupltype=surface-tension
>> Andre
>>
>> On Mon, Sep 25, 2017 at 5:38 AM, Own 12121325 
>> 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
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at http://www.gromacs.org/
>> > Support/Mailing_Lists/GMX-Users_List before posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-requ...@gromacs.org.
>>
>>
>>
>>
>> --
>> _
>>
>> Prof. Dr. André Farias de Moura
>> Department of Chemistry
>> Federal University of São Carlos
>> São Carlos - Brazil
>> phone: +55-16-3351-8090
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>
>
>
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Re: [gmx-users] Simulation in NPgT ensemble

[Own 12121325]

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 :

> it is quite well explained in the manual, pcoupltype=surface-tension
> Andre
>
> On Mon, Sep 25, 2017 at 5:38 AM, Own 12121325 
> 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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
>
>
>
>
> --
> _
>
> Prof. Dr. André Farias de Moura
> Department of Chemistry
> Federal University of São Carlos
> São Carlos - Brazil
> phone: +55-16-3351-8090
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Simulation in NPgT ensemble

[André Farias de Moura]

it is quite well explained in the manual, pcoupltype=surface-tension
Andre

On Mon, Sep 25, 2017 at 5:38 AM, Own 12121325  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
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.




-- 
_

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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[gmx-users] Simulation in NPgT ensemble

[Own 12121325]

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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