[gmx-users] RE: how to fix molecules and give different

Vitaly Chaban vvchaban at gmail.com
Thu Jul 17 08:06:27 CEST 2008

>       Thanks for your reply.
> >      Do fixed molecules have a temperature? What temperature is in fact?
>        Yeah, I want to give all fixed molecules a temperature. The
>temperature in  left box is 253K, in right box is 283K. So there is 30K
>gradient between these two boxes. The middle ice should melt from right to
>       So, you mean to fix molecules and assign temperature can be found in
>       BTW, could you suggest  me any example to refer to ? Thanks.


What is temperature at the microscopic level? - I make hints again.

For you situation, you just have to define the three groups and assign
the wanted temperature (to generate velocities at the start) to each
of them. Be careful with thermostats, the simulation should be in NVE
in the simplest case. No fixed parts are not possible here.

As for technical details, you may open 'grompp.mdp' of any example
provided with gromacs and find the keys (they are accompanied by
comments) where the 'groups' are mentioned. Then consult the manual
about the correct syntax.


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