> That's exactly the problem. And no, there isn't any problem with
> ccptraj according to this.
>
> Yes, we have been made this option you suggest, but we wanted to skip
> these steps, avoiding the equilibration of the box again. I know it's
> difficult what I propose, but only to know if cpptraj had this option.
There is no way you can rotate a single unit cell in a periodic
orthorhombic box; it would bump into its images. You can rotate the
entire periodic system, but this will not do what you want (i.e. orient
the molecule along the long axis). If you are concerned about
re-equilibration, either start with a large enough more spherical box
(truncated octahedron) or you will have to re-solvate. Programs like
PackMol may do a better job of initially solvating. If you really need
long rectangular box you may have to restrain the system to keep it
oriented along the long axis as natural molecule rotation on nanoseconds
time scales is expected... --tec3
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Received on Thu Sep 13 2012 - 12:30:05 PDT
