Vijay,
In the latest release of Amber 12, we have included a couple new options for simulating bilayers. In particular, there is now constant surface tension available, which has been used for lipid simulations. Feller et al in J. Chem. Phys. 1999 have a good description of constant surface tension.
There is anisotropic pressure coupling as well as a new option for semi-isotopic pressure coupling. Semi-isotopic pressure coupling combines the pressure in the XY (or XZ or YZ) direction independent of Z direction (or Y or X) direction.
What I think you want is a combination of semi-isotropic pressure coupling and a constant surface tension for your simulation of the bilayers. Many parameter sets (except parameter sets developed for a tensionless ensemble) have used this ensemble for simulation. The Amber 12 manual includes more details about how to set this.
Ben Madej
Walker Molecular Dynamics Lab
On May 2, 2012, at 6:31, "Ross Walker" <ross.rosswalker.co.uk> wrote:
> Dear Vijay,
>
> I suggest taking a look at the constant surface tension options in AMBER
> v12.
>
> Check page 26 of the AMBER 12 manual here:
> http://ambermd.org/doc12/Amber12.pdf
>
> This will let you set specific surface tensions in one plane which I believe
> is what you want to do here.
>
> You can find details on upgrading to AMBER 12 here:
> http://ambermd.org/#Amber12
>
> All the best
> Ross
>
>> -----Original Message-----
>> From: Vijay Manickam Achari [mailto:vjrajamany.yahoo.com]
>> Sent: Wednesday, May 02, 2012 4:26 AM
>> To: Amber mailing List
>> Cc: Rauzah Hashim
>> Subject: [AMBER] anisotropic pressure in bilayer simulation
>>
>> Greetings,
>>
>> I am simulating lipid bilayer system in constant pressure.
>> For this I use the input file as below
>> Dynamic Simulation with Constant Pressure
>> &cntrl
>> imin=0,
>> irest=1, ntx=5,
>> ntxo=1, iwrap=1, nscm=1000,
>> scnb=1.0, scee=1.2,
>> ntt=2, tempi=300.0, temp0=300.0, tautp=2,
>> ntb=2, ntp=2, taup=2,
>> ntf=2,ntc=2,
>> nstlim=100000, dt=0.001,
>> ntwe=100, ntwx=100, ntpr=100, ntwr=-50000,
>> ntr=0,
>> cut = 8
>> /
>>
>> Here I would like to ask about the meaning for flag ntp=2.
>>
>> I understand from AMBER 9 manual that :-
>>
>> " ntp =2
>> md with anisotropic (x-,y-,z-) pressure scaling: this should only be
>> used with orthogonal boxes (i.e. with all angles set to 90o).
>> Anisotropic scaling is primarily intended for non-isotropic systems,
>> such as membrane simulations, where the surface tensions are differ-
>> ent in different directions; it is generally not appropriate for
>> solutes
>> dissolved in water."
>>
>> For making my question more clearer, I shall define z axis: as a line
>> from bottom to up of this page, x-axis: as a line from left to right of
>> this page and y-axis: as a line pass through this page and away from
>> the reader"
>>
>> Well, what I am curious about is regarding the pressures along xy, yz
>> and xz. For example, in bilayer system, we have two leaflets of layers
>> arranged in a way that, the lipid chains meet each other at the center
>> of the bilayer and the polar part of the lipid pointing away from
>> center at both sides. Normally, in this kind of arrangement, the long
>> molecular axis of lipid arranged in parallel with the z-axis of the box
>> and the polar moiety of the lipid span throughout xy plane direction of
>> the same box.
>>
>> If I use ntp=2 flag, the pressures along the xy direction and top &
>> bottom of the lipid layer should be different. Concerning this matter,
>> I would like to know how does this pressure differences at different
>> sides (top & bottom and lateral) can be further controlled? Meaning if
>> I want to apply more pressure at lateral direction compared to the top
>> & bottom of the lipid layer, how I can achieve this ?
>>
>> Appreciate any help in advance.
>>
>> Regards.
>>
>>
>>
>> Vijay Manickam Achari
>> Chemistry Department,
>> University of Malaya,
>> Malaysia
>> vjramana.gmail.com
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>
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Received on Wed May 02 2012 - 09:30:04 PDT
