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: [email protected] [[email protected]] on behalf of Mark Abraham [[email protected]] 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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