I'm working with a protein in water and I used periodic boundary conditions in three dimension. At first the initial system was minimized, then I followed Justin's protocol. The system was equilibrated in a first stage nvt for 1 ns and in a second stage npt for 1 ns (with restraints). Then the production stage had been done with 100ns.
When I visualize the trajectory results in vmd, I have a problem with the adsorption layer. During the production trajectory, water molecules had spread very much and actually no adsorption happened. The size of the box increases a lot in the beginning of the pvt equilibrated stage (it was 341 nm³ and it becomes 351nm³) and I can't understand that. Why are the water molecules spreading so much? Why don't they constitute an adsorption layer? Any help would be appreciated. Thanks. -- *Yara Pereira Cerceau Alves* Graduanda em Engenharia de Alimentos Bolsista PIBIC/CNPq Universidade Federal de Viçosa - UFV/MG (32)99751550 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
