[gmx-users] eliminating forces on certain direction

[Mark Abraham]

吴鹏 wrote:
> Hi Mark,
> 
> Haha. Yes, your words is right. My objective is to study the interaction 
> between ions and walls. I think the ions may be attached in the wall so 
> the velocity getten from MD simulation is always bigger than the 
> continuum theory's prediction. So I want to build a simulation on which 
> ion can not be attached to the wall. My methods is to reduce the 
> interaction of wall and ions on flow direction. That's my obeject. Any 
> suggestion on that? Thanks in advance.

Probably not, but you'd have to use more precise descriptions than 
"attached in/to the wall" :-) Basically any time you make some 
perturbation to the physics of some force field, you would need to do a 
lot of spadework proving that you haven't produced a (garbage in => 
garbage out) system.

Mark

> On Mon, Oct 12, 2009 at 8:45 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> 
>     ?? wrote:
> 
>         Hi GMX users,
> 
>         I am doing a modified simulation which requires to eliminate an
>         interaction at certain direction while remain the interaction at
>         other directions. Since the itp files contain the C6 C12 of the
>         interaction, it is impossible to only remain the interaction a
>         one direction while eliminating the interaction at other
>         directions. I am thinking of hacking the code while I have no
>         idea of how to do it. Any suggestions on that? Thanks in advance.
> 
> 
>     Start by describing your actual objective in general terms, and not
>     pre-supposing the form of the solution (i.e. manually changing
>     certain interactions). The above sounds like a recipe for disaster,
>     even if you could make it work :-)
> 
>     Mark
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