On Tue, Nov 29, 2005, Ilyas Yildirim wrote:
> icfe=2, klambda=6, clambda=0.5
...
> vlimit exceeded for step 218 ; vmax = 22.6949147823007
>
> Coordinate resetting (SHAKE) cannot be accomplished,
>
> I am not sure why I am ending up with this kind of an error. I
> first thought that the modified .frcmod might be the reason, but this
> mod.frcmod file is working fine with AMBER 8. I have checked out the
> .mdcrd trajectories, and the -NH2 and -O-(DH)2 parts of the structure is
> doing really weird stuff.
Have you run long-ish equilibrations at both endpoints? You should always
do
this first. Look at the trajectories visually...see if you can find out
what
the "really weird stuff" is coming from.
How big are the values of DV/DL that you get? Big values indicate that a
single geometry cannot simultaneously accommodate both endpoint
potentials.
Ideally, you want the optimized geometries of the two endpoints to be
pretty
similar to one another. Another obvious test is to set icfe=klambda=1, to
make sure that there is not something arising from the new code you added.
...dac
Received on Wed Apr 05 2006 - 23:49:47 PDT
