[gmx-users] RE: Energy conservation in collision

Berk Hess gmx3 at hotmail.com
Fri Apr 27 17:40:54 CEST 2007

>From: Janne Hirvi <janne.hirvi at joensuu.fi>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] RE: Energy conservation in collision
>Date: Fri, 27 Apr 2007 18:18:02 +0300
> >>Hello gmx-users!
> >>
> >>I am still struggling with the energy conservation in the system where a
> >>water droplet (consisting of rigid molecules) collides with a frozen
> >>structured surface. The total energy is well conserved at the beginning 
> >>simulation when the droplet is approaching the surface and once again 
>when the
> >>droplet is stabilized on the surface, but the drift or fluctuation in 
> >>total energy is observed between these extremes.
> >>
> >>The total energy of the system (~300 000kJ/mol) decreases slightly
> >>(<100kJ/mol) at the collision and on non-wetting surfaces (water droplet 
> >>intrude to the pores of the surface) part of the energy reverts quickly
> >>causing a sharp peak in the energy curve. This could indicate an 
> >>error at the collision due to the large time step, but equal behavior is
> >>observed with the time steps of 2.0fs and 0.5fs.
> >>
> >>On the wetting surfaces (water droplet intrude to the pores of the 
> >>the center of mass motion of the droplet come to a stop at the collision 
>as in
> >>the case of non-wetting surface and sharp decrease in the total energy 
> >>observed. However, now none of this energy is reverted and the total 
> >>stabilize to this value until the water molecules starts to intrude to 
> >>pores of the surface. The total energy decrease slowly in conjuction 
>with the
> >>slow sinking of the height of the center of mass of the water droplet 
> >>the bottom of the pores is reached. After the bottom of the pores is 
> >>energy will stabilize to the corresponding value which is about 
> >>lower than atthe beginning.
> >>
> >>Decreasing the time step from 2.0fs to 0.5fs have no influence for the
> >>energy conservation and somehow the problem seems to be connected to
> >>water-surface interactions: on the wetting surfaces (more water-surface
> >>interactions) a drift is observed instead of a sharp peak of non-wetting
> >>surfaces (less water-surface interactions). Any ideas how I could 
> >>complete energy conservation?
> >>
> >>Thanks for your time and help,
> >>
> >>Janne
> >
> > What kind of interactions are you using?
> > Plain cut-off for Coulomb and LJ will give bad energy conservation.
> > For your system you probably want to use shifted LJ and Coulomb 
> >
> > Berk.
>I am using PME with slab correction for Coulombic interactions and plain 
>for Lennard-Jones interactions. Neighbor lists are updated every time step 
>to the use of plain cut-off for LJ interactions. This actually gives really
>good energy conservation at the beginning of the simulation, when the 
>is approaching the surface and once again when the droplet is stabilized on 
>surface, but the problems exist between these "stable situations".

You don't specify how you made your surface,
but I assume it would be with LJ particles.
Then you have jumps in the energy with a cut-off, since the LJ potentials
is not zero at the cut-off. This will result in lower energies at contact.

Use a shifted potential, in that way you can also set nstlist to something 
like 10
which will speed up your simulations.


Talk with your online friends with Messenger 

More information about the gromacs.org_gmx-users mailing list