[gmx-users] Protein rotation in triclinic waterbox

Anthony Armstrong armstron at queen.med.jhmi.edu
Wed Jul 19 18:44:52 CEST 2006


I'm hoping to get some tips on removing protein rotation inside a
triclinic water box.  Apologies if this has been covered recently, but
the most recent discussion I've been able to track down is a thread from
2003 which stated a patch was available to prevent such rotations and an
algorithm would be formally implemented into GROMACS "in the near future"
(Tsjerk Wassenaar t.a.wassenaar at chem.rug.nl Tue May 20 13:52:00 CEST
2003).  Has the implementation occurred?  If I use comm-grps = Protein and
comm-mode = angular?  Of course I'm in the process of trying it, but
thought some kind person from the Gromacs community might be able to save
me some time if it is going to fail.  Thanks in advance.


Anthony A. Armstrong
Department of Biophysics and Biophysical Chemistry
Johns Hopkins University School of Medicine
725 North Wolfe Street
Baltimore, MD 21205
410-955-0637 FAX
armstron at groucho.med.jhmi.edu

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