Periodic boundary condition...

[Kasra Momeni]

Hello,

I was wondering how I can setup a system with periodic boundary conditions along all directions.
I would appreciate if you explain it with example.


With best regards,
Kasra.

[Peter Eastman]

Just call setDefaultPeriodicBoxVectors() on your System to set the periodic box dimensions, then call setNonbondedMethod() on your NonbondedForce to select what method to use.

Peter

[Kasra Momeni]

Hello Peter,

Here are the lines of code that I have used for my simulations. I would appreciate if you let me know whether they are correct or not?

Thank you,
Kasra.

omm->system = new OpenMM::System();
Vec3 X = OpenMM::Vec3(32.49,0.0,0.0);
Vec3 Y = OpenMM::Vec3(0.0,32.49,0.0);
Vec3 Z = OpenMM::Vec3(0.0,0.0,51.41);
omm->system->setDefaultPeriodicBoxVectors(X, Y, Z);

[Peter Eastman]

That looks fine. It's a little more wordy than it needs to be, though.

Vec3 X = OpenMM::Vec3(32.49,0.0,0.0);

is exactly equivalent to

Vec3 X(32.49,0.0,0.0);

Peter