[gmx-users] eliminating forces on certain direction

[吴鹏]

Hi Mark,

What you said reminds me to think deeply about my speculation. Thanks for
your remind and I hope to discuss it with you when I get some ideas on that.

Peng Wu

On Tue, Oct 13, 2009 at 10:02 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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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>>
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