Hello all,
I am trying to experiment with NMR refinement protocols for protiens. These protocols are based on ensemble refinement where N proteins are simultaneously simulated and before every integration step, a force is added to the atoms in addition to the force computed from the force field.
So in MD terms here are the steps :
1). Initialize N system simultaneously with velocities. (Normal MD step)
2). Given the current position of atoms in N systems, calculate a force to be exerted on every atom of every protein.
3). Add the custom force to the force derived from the forcefield.
4). Perform an integration, update velocities and positions and repeat.
I have attempted this problem in Gromacs which already has simultaneous simulation implemented (with -multi option) but adding the custom force (and computing the force) is very tedious and not very encouraging. I think LAMMPS might come in handy.
From what I looked around in documentation, adding a custom force on top of the existing force could be achieved with minimal coding but I did not find much information about simultaneous simulations. Can you please refer me to any documentation or tutorial which does simultaneous simulations? Should that be achieved by scripting?
Thank you,
Santhosh