Re: keeping a protein in a solvation box

From: Axel Kohlmeyer (
Date: Tue Jun 12 2012 - 22:16:30 CDT

On Tue, Jun 12, 2012 at 11:03 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?
> 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. it is how periodic boundaries work.
think of you are simulating not a single box, but an
infinitely large crystal. where your simulation cell is
replicated over and over again. this is how the interactions
are compute. have a look at the material posted here:


> 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
> protein
> beneath  # write your atom selection as per the user's manual
> Is that correct.
> Thanks very much for your help and patience!
> Eddie

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.

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