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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Received on Wed May 02 2012 - 07:00:03 PDT
