[gmx-users] protein folding / pbc

Shi, Huilin huilshi at imail.iu.edu
Tue Apr 10 19:22:41 CEST 2012

So if I wanna run a simulation to unfold the protein, I need make a big box that is large enough so that the unfolded protein is still smaller than the box in any dimension. Is this correct?


From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Mark Abraham [Mark.Abraham at anu.edu.au]
Sent: Tuesday, April 10, 2012 11:54 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] protein folding / pbc

On 11/04/2012 1:24 AM, Shi, Huilin wrote:
Hi All,

I have a question about periodic boundary conditions (pbc) when running a simulation to unfold a protein from its native structure.

I set up pbc with the starting structure which is compact.
When defining the box we use editconf and set up the -d 1.0 as the distance from the protein to the box edge.
It is said that "a protein should never see its periodic image".
If during the simulation the protein starts unfolding, the minimum distance from the protein to the box edge will no longer be 1.0 nm.
And it is possible that the length of the protein is even longer than the box dimension and the protein may "see" its periodic image in the neighbored box.
Is this going to be a problem?

Yes, if you don't allow for it from the start. Some test simulations with implicit solvent are probably priceless here.

I am also confused that it is also said that "(parts of) the molecule(s) diffuse out of the box is not a problem".
Is this conflicted with "a protein should never see its periodic image"?

Sometimes - can depend on orientation of molecule wrt box.

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