[gmx-users] Protein rotation in triclinic waterbox

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jul 19 21:15:24 CEST 2006

Hi Anthony,

You can download gromacs v3.1.4 or v3.2.1 with roto-translational
constraints from http://md.chem.rug.nl/~tsjerk/GMX/
Unfortunately I haven't had time to get this in the official distribution yet.
In the patched versions, roto-translational constraints are turned on
if a line is added to the .mdp file stating

rototr = yes

In addition, a reference structure is needed, named ref_conf.gro,
which should correspond to the selection of the protein to be used for
the removal of rotations. Unfortunately, at present it is required
that this part of the protein is listed first in the .gro/.tpr file.
This should be fixed at some point, but hey, it wasn't mny patch in
the first place. The group responsible for the constraints is that of
Andrea Amadei in Rome.

If any help is required in setting up a simulation (it's really not
that difficult), I'd be most happy to help a bit. Contact me off list
in that case.

Hope it helps a bit,


On 7/19/06, Anthony Armstrong <armstron at queen.med.jhmi.edu> wrote:
> Hello,
> 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.
> Tony
> Anthony A. Armstrong
> Department of Biophysics and Biophysical Chemistry
> Johns Hopkins University School of Medicine
> 725 North Wolfe Street
> Baltimore, MD 21205
> 410-955-8715
> 410-955-0637 FAX
> armstron at groucho.med.jhmi.edu
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

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