On 1/10/13 9:28 PM, Tom wrote:
Dear Gromacs Users,
I want to use dihedral constraint in gmx.
First, you should understand that constraints and restraints refer to very
different ideas:
http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
I directly type the following onto my topol.top file :
--------------------------------------
[ dihedral_restraints ]
; ai aj ak al type label phi dphi kfac power
; phi C'(n-1) - N - CA - C'
506 505 502 503 1 1 180 0 1 2
--------------------------------------
Do I also need to add these to *mdp file?
---------------------------------------
dihre = yes
dihre_fc = 15000
-------------------------------------
Everything you need to know is either in the manual or on the website:
http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints
Because I only need to contraint some of the dihedrals,
I will not constraints all of them.
If I add the above on *mdp file, will all the dihedrals be constrainted?
A simple test should be very illuminating. You will get a dihedral restraint
energy written to the .log and .edr files, and either your dihedral will be
restrained or not (easily measured by g_angle).
Another quesiton is what is the format of this dihedral constraints
on *rtp file? How about the angle constraints? That would save a lot
of work if pdb2gmx can automatically add these constraints to *top file.
That's what genrestr is for.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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