Re: [AMBER] thermodynamic integration

From: <>
Date: Sat, 3 Apr 2010 11:02:45 -0400 (EDT)


I would suggest to run all equilibration with TI switched on already,
because you want to equilibrate with the exact same potential function
that you run production with.

It is possible to build a TI system with two preequilibrated prmtop files,
but it will be tricky to get all the coordinates to align.

Kind Regards,


On Sat, April 3, 2010 2:00 am, Hyma vathi wrote:
> Dear Amber Users,
> I need help regarding doing thermodynamic integration in Amber. I am
> confused when to give the TI commands. In the tutorial A9 i.e.,
> "Thermodynamic integration using softcore potentials". Do we need to give
> TI
> commands in the first minimisation file itself or do we need to perform
> the
> minimisation, equilibration and then give the TI commands in the
> production
> file. Thank you in advance.
> Hymavathi,
> MS(Pharm),
> Mohali,
> _______________________________________________
> AMBER mailing list

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

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Received on Sat Apr 03 2010 - 08:30:02 PDT
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