[gmx-users] minimum number of atoms required.
karamyog.singh at gmail.com
Mon Jul 10 09:50:33 CEST 2006
yes i have used gen_velocity = yes. when it did not work with this i gave
the system a velcity of my own. It did not move even then.
even after removing the restrictions oon center of mass motion, that is
after setting comm-mode = None, the particle does not move.
any idea why?
On 7/10/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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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