[gmx-users] Dihedral angle restraints
Antonia Mey
ppxasjsm at nottingham.ac.uk
Tue Dec 4 17:49:39 CET 2012
Dear Gromacs users,
I have a question regarding position restraints on dihedral angles.
I would like to restrain the positions of phi and psi dihedral angles and on top of that increase the potential barrier which needs to be over come in order to go from one conformation to the next. (I.e. I want to add an additional potential term for all common dihedral minima that can be deduced in the Ramachandran diagram, say for \beta, \alpha', \alpha_R and PII)
What I understand so far:
I can add a restraining potential of the form given by equation 4.76 in the user manual.
In the topolgy file I specify the atoms and angle I want like this:
[ dihedral_restraints ]
; ai aj ak al type label phi dphi kfac power
;phi
5 9 7 8 1 1 -70 10 1 2
;psi
9 17 15 16 1 1 150 10 1 2
and in the mdp file I have added this line:
;dihedral restraints
dihre = yes
dihre_fc = 100 ;(adjustable accordingly)
Ideally I want multiple restraints for these angles such that for phi I may have a restraint at -170 and -80 and for psi around 20 and 160 or something along those lines. Do I then just use the function type of 9 in order to do that?
As mentioned above, on top of that I want the minima of these angles to be embedded in a further potential, so that on top of the restraints I have an expression like this for the dihedral angles:
U(\phi, \psi) = 0.5*k(d\phi-\phi)^2 + \sum_{i=1}^nA_{\psi i}exp(-(\psi-\psi_i)^2/2\sigma^2_{\psi,i})
as was defined in this reference:
http://www.pnas.org/content/102/39/13749
Is it possible to achieve this without tempering with the forcefield? I know exactly where i want to place the minima of the potential and how strong I want them to be. Is the tabulated method for dihedrals the correct approach?
I would simply evaluate my U(\phi\psi) at intervals of 10 degrees between -180 and 180 degrees, evaluate the derivative of that function. Then save them in a file table_d0.xvg in the following format:
angle U(\phi\psi) U'(\phi\psi)
:
:
and so on.
Do this for say my 4 constrains corresponding to structures like \betasheet \alpha ' \alpha_R and PII (So I end up with 4 files named table_d0, table_d1, table_d2 and table_d3)
Before I dive into doing something that isn't correct I wanted to clarify this.
Any help would be greatly appreciated!
Best,
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