Dear GMX users, I am trying to simulate a flow of protein over and along a surface structure. To do this, I have a box which is very long in its x direction, relatively small in its y direction and its z dimension is limited by an artificially created surface. These proteins will move in the positive x direction, starting at around x=0, and move towards the surface structure. At this point the protein will either pass along the structure, or adhere to it through LJ/Coulomb interactions. There will also be interactions between the (many) proteins flowing. Essentially, I’m trying to create a flow.
However, I’m unsure on how to do this. If I set the proteins as a acc-grps, they will continue to accelerate even after they have adhered to the surface, essentially pulling them off. Is there a way to set acc-grps for a specific amount of time or distance? After which their velocities will guide them towards the surface structure? Or can I give these proteins a starting velocity after which they just flow? Any ideas? Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
