Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"

From: David A Case <>
Date: Thu, 3 Oct 2013 12:08:47 -0400

On Thu, Oct 03, 2013, 冉挺 wrote:
> In my mind, I use the miniminzed structure to produce and
> and then run TI simulation respectively, is that right? or should I
> use the two unminimized structure and to minimized first
> respectively and then run TI simulation respectively.
> In addition, I suppose TI simulation should be run after the molecular
> system has been heated and reachs the equlibrium state, so if all lamda
> window TI simulations can be carried out based on the same equilibrated rst
> file?

TI runs on a mixed potential energy surface, but otherwise equilibration takes
place as normal. It is not quite clear (to me!) what you are asking here.

As the code tells you, you *must* have *exactly* the same coordinates for the
common atoms in V0 and V1. You cannot (for example) minimize one structure
in the V0 force field, and the other in the V1 force field, then use those
as starting points.

For your second question: you need to equilibrate the system anew for every
value of lambda. You cannot use a single "equilibrated rst file" for all
lambda values. The force field is different for each lambda, and hence the
equilibration must be re-done.

...hope this helps...dac

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Received on Thu Oct 03 2013 - 09:30:04 PDT
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