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 - 04:30:03 PDT
