On Wed, May 25, 2011, arikcohen wrote:
>
> I will be most thankful for any help in the following: I would like to
> run a minimization while constraining a dihedral angle using LBFG.
> Therefore, I would kindly like to know whether it is possible and if so
> how to make the .in file . My input file is the following,
What happens when you run this? It's usual to try at least some experiments
on your own before asking for help.
>
> All atom minimization
> &cntrl
> imin=1,
> ntmin=3,
> maxcyc=90000, ncyc=10,
Why do you want 90000 cycles? Also, the minimization will stop at the default
rms gradient, which is rather high. If, for some reason, you want a very low
gradient, you need to set the drms target to something other than its target.
> ntb=1,
> igb=0,
> cut=10.0,
This will lead to problems, since the energy function will change
discontinuously when the non-bonded list is updated, and minimization will
fail. You need to set cut to 999., or some value much bigger than the size of
your system.
> ntr=0,
> nmropt=0,
> /
> &lmod
> xmin_method="LBFGS"
> /
>
Your input doesn't seem to have any dihderal restraints.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 25 2011 - 15:00:03 PDT
