[gmx-users] questions on acceleration
Jennifer.Williams at ed.ac.uk
Fri Jul 17 19:08:47 CEST 2009
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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