Hi,
> I would like to pertube system (7 residues) in vacuum to nothing, but I am
> forcing several problems:
what happens when you look at your system trajectory? If you have
restraints on and the molecule still moves beyond the virtual box
something strange is going on...
> On the other hand, I would like to run all TI simulations in amber 11.
> Since ifsc=2 option is no more implemented in this version, I would like
In Amber11 doing a full soft core transformation of a molecule to
'nothing' would amount to a deltaG of zero, hence ifsc=2 was removed as it
is no longer necessary. In fact the transformation does not really
'remove' the molecule, it shifts it into a state not interacting with its
environment, 'quasi vacuum'. Doing that starting in vacuum just means that
nothing really changes. What kind of thermodynamic cycle would require the
calculation that you describe?
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed May 25 2011 - 07:30:04 PDT
