From: Vermaas, Joshua (
Date: Tue May 15 2018 - 18:07:47 CDT

Hi Fan,

I think the "minmax" argument described in the solvate documentation would do what you want. -t does what you describe, and pads around your solute evenly. With minmax, you specify the size of your box (replace xmin, xmax, etc with your preferred values):

solvate ubq.psf ubq.pdb -o solvated -minmax [list [list $xmin $ymin $zmin] [list $xmax $ymax $zmax]]

If you choose the appropriate parameters, that will fill the "top" of your box in addition to the space around your two molecules.

The density of this waterbox will likely be wrong, but that's ok. Equilibrate at constant pressure for a little bit and the box size will settle down, after which you can switch to constant volume simulation if you want to.

Unphysical bonds can mean alot of different things. Are there atoms now placed at the origin? Basically, solvate calls psfgen, so if there is something strange lurking in your psf-pdb pair that psfgen doesn't like, you can get strange things to happen.


On 2018-05-15 16:47:24-06:00 wrote:

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--_000_DM6PR09MB2922B4518E22C13557D3FDADE4930DM6PR09MB2922namp_--