VMD-L Mailing List

From: Steven Neumann (s.neumann08_at_gmail.com)
Date: Mon Sep 10 2012 - 09:45:42 CDT

Dear All,

I want to simulate a protein line chain in explicit solvent model. for
this purpose I want to solvate it in either dodectahedron with PBC or
in sphere water box. Would you suggest something?
I tried to use the script from NAMD tutorial ( wat_sphere.tcl )and my
protein in solvated in the rectangular box after using it. How can I
fix it?

thank you,

Steven