Hi, I'm trying to do an SMD simulation to generate configurations for Umbrella sampling. I want to pull two groups together.
I'm having trouble understanding why the pulled distance must smaller than the half the *shortest* box-vector length. I know that distance is calculated taking periodicity into account and that distances/vectors between objects should obey the minimum image criterion. Hence. if the restraint distance becomes larger than the box length you'd get discontinuities in the pulling. But I thought this is checked component-wise. i.e dx = x_i - x_j < Lx*0.5 dy = y_i - y_j < Ly*0.5 dz = z_i - z_j < Lz*0.5 but instead what seems to be necessary is that | r | = sqrt(dx^2 + dy^2 + dz^2) < min(0.5Lx, 0.5Ly, 0.5Lz) Could someone explain why it is not sufficient to check whether dx,dy and dz are smaller than half their respective box vector lengths to avoid discontinuities in the pulling? But instead, we must check if | r | is smaller than half the shortest box vector lengths. I ask because in my system the two groups that I want to pull together are separated a large distance in the x-direction but not that much in the y and z-direction. So accordingly, I made a box that is long in the x-direction but small in y and z but this doesn't work out and I get the error the distance between pull groups is larger than half the box size. Sincerely, Shrinath -- 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.
