Dear Amber Users,
I am trying to do a free energy perturbation
calculation in which a theophylline molecule
"disappears" while in explicit water solvent. I used
a delta lambda value of 0.05 with NRUN = 21, and 1500
steps of equilibration and sampling for each run,
beginning at lambda = 1.
Between lambda = 1 and lambda = 0.2, the accumulated
forward and reverse energies were very reasonable and
were almost of equal magnitude. However, as soon as
it reached lambda = 0.15, the accumulated reverse
energy went from being about +15 to ? -300.
Furthermore, the accumulated forward energy began to
increase from ? -15 to zero, and then began to
decrease again at lambda = 0.10.
My perturbed-state frcmod file for theophylline is
identical to that of the regular frcmod file, except
all the NONBON terms are zero.
Does anyone know what may be causing this bizarre
energy output, and how it may be fixed?
Thank you very much,
Peter Anderson
__________________________________
Do you Yahoo!?
SBC Yahoo! DSL - Now only $29.95 per month!
http://sbc.yahoo.com
Received on Mon Jul 14 2003 - 03:53:00 PDT
