[gmx-users] simulations using structureless surface-2

[Erik Marklund]

27 jul 2007 kl. 09.53 skrev Erik Marklund:

> There was a tutorial on implementing a z-dependent electric  
> potential on the gromacs web page not that long ago. It didn't seem  
> that difficult. That should serve as a good starting point for your  
> wall o' carbon.
>

...namely http://wiki.gromacs.org/index.php/Patching_mdrun

>
> 27 jul 2007 kl. 01.56 skrev Mark Abraham:
>
>>> Dear gmx users,
>>> my apologies for the previous post. I will try to rephrase my  
>>> problem.
>>>
>>> Is it possible to introduce a plane in a particular direction,  
>>> for example
>>> in z direction, where molecules interact with it only based on the
>>> perpendicular distance between the molecules and the plane?
>>
>> Yes, this is possible to do, but it is not implemented. Possibly  
>> something
>> in the distance restraints section may do what you want. See the  
>> manual.
>>
>>> Is it also possible to specify the user defined potential for  
>>> interaction
>>> between the plane and molecules?
>>
>> Possible, but not implemented.
>>
>>> The idea is to simulate a surface, for example a graphite  
>>> surface, but
>>> rather than using a detailed atomistic model for it, I would like to
>>> represent it by using a plane with some interaction potentials.
>>
>> If you're not dealing with only a handful of species interacting  
>> with such
>> a surface, you might want to write such code yourself. Otherwise,  
>> you'll
>> need to get your hands very dirty with GROMACS.
>>
>> Mark
>>
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>
> _______________________________________________
> Erik Marklund, PhD student
> Laboratory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,	75124 Uppsala, Sweden
> phone:	+46 18 471 4537		fax: +46 18 511 755
> erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys
>
>
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys