[gmx-users] Re: gmx-users Digest, Vol 27, Issue 30
erwindownunder at gmail.com
Mon Jul 10 12:48:56 CEST 2006
It is a probably a pretty naive answer and you probably tested it
already but have you checked the box size?
> 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.
> > Mark
> I am sorry. The particle does move if I give it an initial velocity myself
> after setting comm-mode = None. However with gen_velocity = yes, It gives
> the atom a velocity of zero.
> thanks for your help.
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