[gmx-users] simulations using structureless surface-2
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
27 jul 2007 kl. 01.56 skrev Mark Abraham:
>> Dear gmx users,
>> my apologies for the previous post. I will try to rephrase my
>> Is it possible to introduce a plane in a particular direction, for
>> 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
> in the distance restraints section may do what you want. See the
>> Is it also possible to specify the user defined potential for
>> between the plane and molecules?
> Possible, but not implemented.
>> The idea is to simulate a surface, for example a graphite surface,
>> 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,
> need to get your hands very dirty with GROMACS.
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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
More information about the gromacs.org_gmx-users