Hello guys, I have tried to calculate the PMF for a dimer in a rectangular box of dimensions 3 x 3 x 7. However, the simulation stops when the COM separation is above 1.49 (ie half of the smallest dimension of the box. Since I am pulling along the Z axis at a distance that would be up to 3.5 nm.
I've tried both pull_geometry, distance and direction, to try to get around this, but I have not been successful. Do I have to use the dimensions of the box as twice the COM distance (in my case: 5 x 5 x 5; to give me r_max = 2.5nm)? Some of you could give me a hand? DIRECTION pull = umbrella pull_geometry = direction pull_dim = Y Y Y pull_group0 = mol_0 pull_group1 = mol_1 pull_rate1 = 0.01 pull_vec1 = 0.0 0.0 1.0 pull_k1 = 3000 DISTANCE pull = umbrella pull_geometry = distance pull_dim = Y Y Y pull_group0 = mol_0 pull_group1 = mol_1 pull_rate1 = 0.01 pull_vec1 = 0.0 0.0 0.0 pull_k1 = 3000 _______________________________________ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Tel.: (12) 3309-9573 Página: sites.google.com/site/fileti/
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
