[gmx-users] questions on acceleration

[Jennifer Williams]

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?


Thanks


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