Re: Salvation of non-orthogonal box

From: HEMANTH H 18310019 (hemanth.h_at_iitgn.ac.in)
Date: Thu Sep 12 2019 - 21:38:40 CDT

Dear Raziyeh,

You cannot solvate a hexagonal box natively in VMD. Rather, you should
solvate it as a rectangular box and then cut out the extra water molecules.

Hope this helps.

Hemanth

On Fri 13 Sep, 2019, 12:16 AM Yousefi, Raziyeh, <rayousef_at_utmb.edu> wrote:

> 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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