Salvation of non-orthogonal box

From: Yousefi, Raziyeh (rayousef_at_UTMB.EDU)
Date: Thu Sep 12 2019 - 13:43:56 CDT

Dear NAMD users,

I am trying to solvate a unit cell, hexagonal structure, using 'inorganic builder' -> 'solvate box' with my system basis vectors, but for many atoms at the boundary, the built solvated structure contains huge binding lengths (‘lines’ in visualization) stretching from one side of the box to the other side. Same happens when I try to solvate it within a parallelepiped box or even single protein structure in hexagonal or parallelepiped boxes. The unit cell structure seems fine before solvating.

I want to use periodic BC in my simulations. Can anybody help me with solvating my hexagonal structure properly? Thanks!

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