Dear Erik, The wall which I want to introduce will interact with 9-3 potential only and will have no charges. Will it be more appropriate to calculate it where the nonbonded interactions are calculated in gromacs (nonbonded.c ?) and then update the total potential energy? In principle it sounds "simple" but I totally get lost as soon as I open nonbonded.c Is there any other place where it will be relatively easier to implement it?
With Regards, Gurpreet Singh ------------------------------------------------- University of Dortmund Department of Chemistry Physical Chemistry I - Biophysical Chemistry Otto-Hahn Str. 6 D-44227 Dortmund Germany Office: C1-06 room 176 Phone: +49 231 755 3916 Fax: +49 231 755 3901 ------------------------------------------------- -----Original Message----- From: Erik Marklund [mailto:[EMAIL PROTECTED] Sent: Friday, July 27, 2007 9:54 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] simulations using structureless surface-2 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. /Erik 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 > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > 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 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php