[gmx-users] Minimization and torsion angles
Mark.Abraham at anu.edu.au
Tue Feb 8 01:16:09 CET 2011
On 8/02/2011 2:47 AM, abdullah ahmed wrote:
> I have an input structure with poor torsion angles and after
> minimization with gromacs (both steepest descent and congugate
> gradient) I found that they were not corrected. There is enough free
> space for the torsion angles to be corrected.
> (I am sure of this because when I run the same structure in Insight it
> is able to correct them. Both programs give very similar structures
> with the major difference being the torsion angles.)
> Has this happened because Gromacs potentials do not penalize poor
> omega angles?
Peptide bonds ordinarily have improper dihedrals on them to keep them
close to planar.
> Or have I done something wrong? (I have added by .mdp file at the end
> of the mail)
> Is there a way besides applying a restraint to every torsion angle to
> induce Gromacs to correct them?
EM is a local minimization method, and the result depends on the method
and its parameters. Perhaps choosing a larger step size with
steepest-descent algorithm will fix your issues.
> Thank you in advance for you help,
> ; User spoel (236)
> ; Wed Nov 3 17:12:44 1993
> ; Input file
> cpp = /usr/bin/cpp
> define = -DPOSRES
> constraints = none
> integrator = cg
> nsteps = 2000
> ; Energy minimizing stuff
> emtol = 2
> emstep = 0.01
> nstcomm = 1
> ns_type = grid
> rlist = 1
> rcoulomb = 1
> rvdw = 1
> Tcoupl = no
> Pcoupl = no
> gen_vel = no
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users