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,
Tsjerk
On 7/19/06, Anthony Armstrong <[EMAIL PROTECTED]> 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
[EMAIL PROTECTED]
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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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