some problem about velocity command

Hi All,

I am doing simulation about hydrocarbon. I want to set speed to the molecules (and every atom in the molecule have the same speed). Meanwhile different molecules have different random speed by gaussian. Now I don’t know how to realize the command .Using velocity and group command together? Thanks for your reply.

Kely

Hi All,

I am doing simulation about hydrocarbon. I want to set speed to the
molecules (and every atom in the molecule have the same speed). Meanwhile
different molecules have different random speed by gaussian. Now I
don't know how to realize the command .Using velocity and group
command together? Thanks for your reply.

what is the purpose for this?

unless you have a dilute gas, i cannot see a good reason, as for any
dense system, atoms would bump into each other and thus the initial
effect to have no rotations would extremely quickly vanish and you
could not tell the difference between a per molecule and a per atom
initialization.

axel.

Hi axel, my only purpose is to simulate the molecule movement so i wish the molecules unbroken during the process. And I don’t know if i set random speed to all the atoms, would the molecule break into pieces?​ So i wonder if i set a same velocity in a molecule, i can only see the molecule movement and the molecule would not break down.

the same argument i made before applies here as well. i don't think
there is going to be a difference in initializing per atom velocities
and per molecules velocities and then atoms smashing into each other
because you have a sufficiently dense system. i would expect, that
after a small number of time steps, the result will be
indistinguishable.

if you have worries about molecules "breaking" unexpectedly, then the
reason is more likely something else, e.g. a bad initial geometry or
topology, bad parameters or incomplete understanding of the chemistry
or physics of the state being investigated.

if you want to have a gentler way of assigning an initial temperature,
don't use the velocity command, but start at 0K and use a thermostat
fix with a temperature ramp.

axel.

Thanks axel , i will try for it to start at 0K and see the result. :slight_smile: