[gmx-users] user-defined proper dihedrals and restraints

Chris O'Brien obrien at CLEMSON.EDU
Thu Oct 17 22:42:24 CEST 2002


I have two questions.  First, is it possible to edit/create a user-defined 
function for proper dihedrals?  My molecule (polylactic acid) is chiral, so 
the dihedral rotation energy curve (phi vs theta) is not symmetric.  Thus, 
a Ryckaert-Bellemans expression can never fit it properly.  It would need 
phase shifts in the theta terms.  If this is possible, where in the program 
would I need to make these additions?  Are there any pitfalls I should be 
aware of?  If I were to make a piecewise (-180 to 0 and 0 to 180) 
expression, do I need to worry about discontinuity or non-differentiability 
at the junction?

Second, is there an easy way to lock (constraint or restraint) a single 
dihedral angle during a simulation?  I saw atom position, bond length, and 
angle restraints in the manual, but no mention of dihedrals.  I was 
thinking that I could lock each trio of relevant atoms (i-j-k and j-k-l) 
into a plane to duplicate the effect.  In the manual it tells how to 
restrain an atom into a plane, but I'm not sure if GROMACS will understand 
my intentions if I do this.  Especially because I don't necessarily want it 
to be, for example, the XY plane but rather the plane defined by the 
starting positions of atoms i, j, and k.  Any ideas?

Thank you,

Chris O'Brien
Clemson University
Clemson, SC USA

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