Dear gromacs users, I'm trying to simulate amphiphilic molecules, building stable structures by non-bonded interactions. I have seen in biological research, membranes and proteins therein are often subject of simulations. A cell membrane, I guess, could be an example of a structure built not by hard-core chemical bonds.
Let's say you know experimentally that molecule X, builds starlike structures! Or a surfactant builds a sphere. Now to simulate this - to see e.g. the diffusion of other molecules in and out - does it make sense to build a sphere of, say 100 - the number you may know again from experiments - in a spherical geometry, and let them deal with eachother by a forcefield, or it's necessary to explicitly fix their positions? If yes, will it give realistic results? In the end one could fix positions of 10, 100 and 1000 molecules as a sphere, though only those with 100 are stable, in lab! I would greatly appreciate any comment, from those who do membranes or other alike predefined structures. Thanks in advance, Peyman _______________________________________________ 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
