[gmx-users] protein folding / pbc

Matthew Zwier mczwier at gmail.com
Tue Apr 10 20:26:59 CEST 2012


On Tue, Apr 10, 2012 at 1:22 PM, Shi, Huilin <huilshi at imail.iu.edu> wrote:
> 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?
> Thanks.
> Huilin
> ________________________________
> 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.
> Mark
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