Dear Gmx Users, I am trying to setup the system of nanotubes with attached polypeptides. I wish to define the equlibrium distance (PMF minima) between them. However in my system, I will have 6 of them in which one is in its quarter in the rectangular each box edge copied across pbc. It is the only one way I can do this as 3 nanotubes form a isosceles triangle. However if I will change the distance between them, I need to change the box size. Is that possible to use in Umrella Sampling with the box which difer in number of atoms and box size?
Or would you rather run first 1) run just 2 nanotubes - one with position restraints and one with harmonic potential, evaluate PMF using umbrella sampling (or sth else?) at different distances and then apply it with a second system 2) made of more of nanotubes to with the distance defined from step 1)? Please, advise Steven -- 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.
