From: Vermaas, Joshua (
Date: Thu Apr 12 2018 - 14:55:26 CDT

What is your reaction coordinate? Normally the positions don't change by just adding water, but some might if you are looking at the center of mass of all atoms or something like that.


On 2018-04-12 09:47:15-06:00 wrote:

My reaction coordinate values are changing from the solvated pdb when compared to the crystal structure. Could anybody suggest me ways of undoing that. The command that i am using for solvation is :
 solvate ubq.psf ubq.pdb -t 5 -o ubq_wb

Sheena Singh