AMBER Archive (2009)

Subject: Re: [AMBER] Thermodynamic Integration and belly

Date: Mon Apr 13 2009 - 11:46:19 CDT


> Does anybody know why in the Amber code ibelly=1 (frozen atoms) and icfe=1
> (thermodynamic integration) are incompatible?
> I changed the code to allow this combination of parameters to run and, so
> far, I haven't seen anything strange, apart from the fact that you have to
> be careful and patient to get to a well equilibrated system.

My personal guess would be that TI and ibelly can coexist as long as the
belly region is exactly the same in both processes and doesn't contain
changing parameters. However, the warning you disabled certainly means
that no one ever tested this assumption and moreover that the TI code was
written without the belly option in mind. The correctness of your results
is therefore absolutely *not* ensured.

Is there a reason you have to use ibelly instead of harmonic restraints?
The later would not only be better tested but in my (and probably many
other peoples) opinion a more realistic description of a restrained

Kind Regards,


Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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