Dear Marck, Will you please give me some suggestions on how to decide whether the probelm is from periodic boundary conditions? Cheers, Acoot
----- Original Message ----- From: Mark Abraham <mark.abra...@anu.edu.au> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Monday, 6 August 2012 10:31 PM Subject: Re: [gmx-users] a residue move in extremely large scale in MD On 6/08/2012 8:58 PM, Acoot Brett wrote: > Dear All, > > I have a protein with about 400 amino acids. I have done a production MD of > it. I find in the 400 amino acids, there is 1 amino acids, during the whole > MD process, this residue moves in a extremely large scope in comparison with > all the other residues. > Do you think this single residue with extremely large-scale movement in the > whole MD has important biological function, or has no biological function? I'd start by proving that it was not a problem with periodic boundary conditions! If real, movement may or may not be indicative of functional significance - the question is impossible to answer out of context. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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
