[gmx-users] minimum number of atoms required.

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jul 10 07:09:56 CEST 2006

karamyog singh wrote:
> Dear users, I have a system with just one atom. I am using periodic 
> boundary conditions. No matter what conditions I use, the atom doesnt 
> seem to move. Are a minimum of 2 atoms required to do a simulation in 
> Gromacs? If I have only one atom and I am using periodic boundary 
> conditions then whether I have interaction potential or not, the atom 
> should move with some velocity. However this does not happen. Can anyone 
> tell me what is the reason for that?

A simulation with only one particle isn't useful - there can be no 
interactions, so whatever the initial velocity is, it will remain 
constant, as will the energy components (unless you are doing something 
weird with an applied electric field, etc). You should however see this, 
but you won't if you have set the option to remove the centre of mass 
velocity - because obviously here your particle is your centre of mass - 
see section 7.3.3.


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