Re: keeping a protein in a solvation box

From: Aaron Oakley (
Date: Tue Jun 12 2012 - 22:26:52 CDT

On 13/06/2012, at 1:03 PM, Dr. Eddie wrote:

Thanks for the info!

Now correct me if I am wrong (and I pretty sure I am) but I can't understand the following. If I have a piece if a protein which is sticking out of my pbc solvated box, say residue 1, then there is no solvant for residue 1 to interact with except the on periodic boundary and in the box. But around residue 1 there is no solvant since it wrap (wrapWater). So it seems it would be in vacuum but not see any surface tension of the solvant due to the pbc. Where is my misunderstanding?

The residue WILL interact with solvent, but it will be with the solvent molecules on the other side of the periodic system.

When I look at this using vmd I see part of the protein leave the box. If I add a periodic image then it looks like the part that left the box is solvated. But as mentioned above this seems like an illusion.

It is NOT an illusion. NAMD calculates interactions across the periodic boundary.

Thanks for pasting the code! I think I have a vague understanding of what it will do. Just so I am clear, if I only have a protein in water and I want to align my protein I need only add
beneath # write your atom selection as per the user's manual
Is that correct.
Thanks very much for your help and patience!

On Tue, Jun 12, 2012 at 6:52 PM, Giacomo Fiorin <<>> wrote:
And at any rate, Eddie, your protein never leaves the box, for as long as you have PBCs enabled. Most of the time you're sure of that, if you want to be 100% sure look into using VMD to wrap the coordinates.

On Tue, Jun 12, 2012 at 7:50 PM, Giacomo Fiorin <<>> wrote:
Thanks Aaron! You beat me to this.

However, I can see another email coming requesting to clarify, so I'm pasting here the example configuration. The last time I sent this to namd-l was a while ago and may not show up easily in a keyword search.

colvar {

    name com
    width 1.0

    distance {
        group1 {
            # write your atom selection as per the user's manual
        group2 {
            # change the position of this dummyAtom if you want a different
            # point as the center
            dummyAtom (0.0, 0.0, 0.0)

colvar {

    name orient
    width 0.05

    orientation {
        atoms {
            # write your atom selection as per the user's manual
        refPositionsFile reference_coordinates.pdb

harmonic {
    colvars com orient
    forceConstant 10.0
    centers 0.0 (1.0, 0.0, 0.0, 0.0)

On Tue, Jun 12, 2012 at 7:45 PM, Aaron Oakley <<>> wrote:
You could use collective variables to remove the rotation/translation component of your macromolecule.


On 13/06/2012, at 8:44 AM, Dr. Eddie wrote:

> Hi all,
> What is the best way to keep a protein inside a solvation box?
> With wrapwater and wrapall on my protein still climbs out of the box (presumably still experiencing solvation due to periodic boundary conditions, but I can't be sure). I'd like the protein to stay in the box. Should I fix one single atom in the protein? Is there a better way than just making an enormous box?
> Thanks,
> Eddie

A/Prof Aaron Oakley
School of Chemistry
University of Wollongong
Northfields Avenue
Wollongong, NSW, 2522
Phone: (02) 4221 4347
Fax:   (02) 4221 4287

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