Dear Professor Case,
This is Henry from Dr. Michael Johnson's lab. In Amber 11/12 user
manual, there is one sentence saying "When using softcore potentials, ë
values should be picked so that 0.01 < clambda < 0.99". I am quite
confused why there is such a setting. Could you kindly offer an explanation
or recommended papers for this?
One interesting thing is I found my previous error (
http://archive.ambermd.org/201208/0390.html), in which the mask atoms
becomes "a spider monster from space" , is due to clambda < and clambda
> 0.99. Alternatively, the softcore potential production run is quite
normal if 0.01 < clambda < 0.99, but not clambda < 0.01 and clambda > 0.99.
If 0.01 < clambda < 0.99 in softcore potential is true, then is there any
recommended way to set the largest and smallest clamda values for a 12
windows TI run and following Gaussian integration? (The corresponding table
is in Amber 12 user manual's "Table 4.1.: Abscissas and weights for
Gaussian integration<
http://i1076.photobucket.com/albums/w454/happypsu4/table41.png>.")
Thanks.
Best,
Pin-Chih Henry Su
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Received on Mon Sep 17 2012 - 16:30:02 PDT
