Correct.
On Tue, Apr 10, 2012 at 1:22 PM, Shi, Huilin <huil...@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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on > behalf of Mark Abraham [mark.abra...@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 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists