Re: AMBER: Re: TI tutorial

From: David A. Case <>
Date: Wed, 29 Jun 2005 07:30:31 -0700

On Wed, Jun 29, 2005, Jiten wrote:
> 1. For the changing in the charges - I make the DELTA.charge column such
> that the charges of the perturbed state is for GLY. (tmp3.tif is the xleap
> editor image) Now do the TI calculations in gas and solvent phase. Find the
> difference. Do I need to carry out 12 windows in both the cases ?

This discussion is not really being very productive I think. I don't
understand why you want to do gas-phase calculations in the first place.
You should think carefully about the thermodynamic cycle you are trying to

"DELTA.charge" is the difference between the charge in the lambda = 0 state
and the lambda=1 state. If you have concerns, study the perturbed prmtop
file to make sure it is getting what you want. Run (short)
simulations with lambda=1, and compare the results to a "standard" prmtop
file that represents the lambda=1 (GLY) state.


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Received on Wed Jun 29 2005 - 15:53:01 PDT
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