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
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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
[EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys
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