Hello, I have 3 short questions regarding adding an acceleration.
1. I want to apply a force in the z direction to some of my molecules to mimic a chemical potential gradient. I read an old gmx_users post where someone wanted to add an external force to their molecules and the advice given was to add a piece of code after the function efield in the code in src/mdlib/sim_util.c . That is, to make a function similar to efield which would do Fsum = Fsum + Fext
Is there any reason for doing this rather than using the accelerate option in the .mdp file?
2. If I do use the accelerate option in the .mdp file, I need to convert the acceleration applied into a force. Just to check?. I assume that if I use F=ma, where F and a are the force and acceleration applied to a molecule, then m should be the mass of that molecule? I.e for a CO2 molecule, m will be 44 a.m.u?
3. If I use the accelerate option under NEMD, does it still make sense to remove the C.O.M?
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