Greetings to All I have a question about a new feature in the cvs code and I was wondering if there was anybody who could give me a hand of a bit of help. Thanks in advanced.
I am working on a project that involves simulation of confined water between two hydrophobic surfaces. I noticed that recently there was an addition to the gromacs source code that would allow for this kind of simulations I downloaded the cvs source code to try out this new feature, ran a small simulation of water with pbc=xy and no surfaces and could see the water evaporate as was expected The problems occurs when I need to add surfaces to the simulation. There are some new variables that I don't know how to set and I have not been able to figure this out from the source code. What are the appropriate values for wall_atomtype? I want to have a LJ interaction between the wall and the oxygen atom in the water molecule. How can I do this with this new feature? In the function do_walls we have (file wall.c) if (ir->wall_type == ewt93) { fac_d[w] = ir->wall_density[w]*M_PI/6; fac_r[w] = ir->wall_density[w]*M_PI/45; } else if (ir->wall_type == ewt104) { fac_d[w] = ir->wall_density[w]*M_PI/2; fac_r[w] = ir->wall_density[w]*M_PI/5; } Where are these factor coming from, is there a reference that I can look at? What would be appropriate values for the variable wall_density? Would these be the appropriate changes to my grompp.mpd file to get this feature working of is there anything else that I need to add? pbc=xy nwall=2 wall_type=9-3 wall_atomtype = ? ? wall_density = ? ? I apologized if these are too many questions!! I realized this a very new feature and probably it is not well tested, yet I would like to try it out and see if I can use this for my project Any help would be really appreciated. Thanks a lot. Kind regards, Manuel Valera ____________________________________________________________________________________ Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo! Travel to find your fit. http://farechase.yahoo.com/promo-generic-14795097 _______________________________________________ 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