Sv: Re: [gmx-users] surface simulation

Peter Ahlström Peter.Ahlstrom at
Mon Nov 3 14:21:32 CET 2008

If vapour pressure is not too high, I think it is physically more
relevant to simulate a CCl_4
slab with periodic boundary conditions suck that you get an infinite
2-slab repeated in the third 
dimension such that you get a vapour slab in between (surface tensions
etc are normally 
measured in equilibrium with the vapour). So, in my opinion, the easiest
thing to do is to simulate 
a slab of CCl_4 together with the vapour (at least you get less
artefacts from bad wall models
in that way). At least that is a somewhat physical system. Normally I do
not think that position
restraints are needed (but I have no experience with CCl_4)


Dr. Peter Ahlström
School of Engineering
University of Borås 
SE-501 90 Borås
Ph. +46-33-435 46 75 Fax +46-33-435 40 08
peter.ahlstrom at
>>> Mark Abraham <Mark.Abraham at> 08-11-03 05:08 >>>
Hongyan Xiao wrote:
> Hi, Mark Abraham,
> I accepted your suggestion on the language.
> I simulated the CCl_4 surface system. In order to simplify model,
> the vacuum replaced the gas phase. Furthermore, I found some paper by 
> other people also deal with the gas/liquid using the vacuum. In 
> vacuum/CCl_4 , can I control the CCl_4 molecule not to run to the
> using the gromacs? For example, using the wall, but I do not set up
> parameters well. Please give me some suggestion. Thanks again!

Some position restraints will keep your surface intact. See the manual 
for details. GROMACS will report how much "energy" is going from the 
restraints and you should check your parameterization by seeing that 
this energy is pretty small.

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