[gmx-users] surface simulation

Mark Abraham Mark.Abraham at anu.edu.au
Mon Nov 3 05:06:17 CET 2008

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, using 
> 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 vacuum 
> using the gromacs? For example, using the wall, but I do not set up wall 
> 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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