[gmx-users] simulations using structureless surface-2

Erik Marklund erikm at xray.bmc.uu.se
Fri Jul 27 09:53:47 CEST 2007

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.


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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