simtk.org

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.

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

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);

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