VMD-L Mailing List

From: fan li (fanliqmul_at_gmail.com)
Date: Tue May 15 2018 - 16:59:11 CDT

Hi every one

I have molecule1 in the middle of my box, and molecule2 at the bottom. Now
I want to fill the other volume not occupied by molecule1 and molecule2. I
tried following command

solvate ubq.psf ubq.pdb -t 5 -o ubq_wb

It created the water around the molecule1 and molecule2, but the molecule2
is already at the boundary of my box,so there should be no waters below it.

(1)How can I fill the other volume not occupied by molecule1 and molecule2
in vmd?

(2)And what is the density of the solvate?

(3)I also noticed that my original psf might be changed after I used the

solvate ubq.psf ubq.pdb -t 5 -o ubq_wb because some non-physical bonds is
generated in the display window? Why it happend?

Fan