AMBER Archive (2006)

Subject: Re: AMBER: Different results for TI calculation

From: David A. Case (case_at_scripps.edu)
Date: Thu Jun 01 2006 - 09:33:32 CDT

On Wed, May 31, 2006, Biswa Ranjan Meher wrote:
>
>
> I performed the charging free energy calculations for both in vaccum and in
> water and got the results close to the tutorial. But unfortunately I got
> much different results when performed for disappearing free energy
> calculation as compared to the tutorial.
>

I don't see anything obviously wrong with your input; maybe someone else will
spot something. You can double-check the prmtop you are using, and look to
see if the system is really well equilibrated. Run a second production run
(starting from the end of the first one) to see if the results change.

I do note that you are starting each equilibration with irest=0; I would
always have used the last step of some system that was as close as possible to
the system I wanted. Make sure your pressures and volumes are
well-equilibrated.

....good luck...dac

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