[AMBER] Fixing few box dimensions in semiisotropic/anisotropic pressure scaling

From: Kyeong-jun Jeong <kjeong23.wisc.edu>
Date: Mon, 15 Apr 2019 20:56:54 +0000

Dear All,

Does Amber18 support giving a hard constraint on some axes of box dimensions while performing semiisotropic / anisotropic pressure scaled NPT simulations?

I would like to simulate a system containing solid-liquid interface in a tetragonal box. The crystal surface is along the xy plane, perpendicular to the z axis.

(orthorhombic periodic box with dimensions a=b, while c is not equal to a or b)

This is a sample mdin file I used which is similar to typical membrane simulations:

semiisotropic npt : density equil
  ioutfm=1, ntwv=-1,

So I used ntp=3, csurften=3 to decouple z-axis from x,y axes, with ninterface=2, gamma_ten=0.0 .

I found that in this NPT simulation, still the X,Y box dimensions can change depending on system condition, even though the change was not severe during the density equilibration compared with change in Z dimension to equilibrate the system density.

For an ensured mechanical stability of the crystal phase, I would like to fix the X,Y box dimensions and only allow Z dimension to change.

Does Amber18 support the feature to give hard constraint on few axes of box dimensions?

or it is just unrecommended to apply X,Y box size hard constraint in the simulation itself?

Thanks a lot,

Kyeong-jun Jeong

AMBER mailing list
Received on Mon Apr 15 2019 - 14:00:02 PDT
Custom Search