Re: [AMBER] how to simulate solute in vacuum with TI

From: <>
Date: Wed, 23 Feb 2011 03:39:59 -0500 (EST)


> with respect to step1, are the simulation conditions such as ¡°cut,
> gamma_ln, ntf, ntc, temp0¡± must identical to aqueous phase? can i modify
> the ¡°cut¡± larger for step1?

The cutoff for the vacuum steps can (and even should?) be larger than for
the solvated systems. The important thing is that both simulations give a
realistic description of your molecule and optimal parameters to achieve
that can be different. The temperature should be the same though, since it
will influence deltaG and you would have to add cooling or warming steps
if two legs of your thermodynamic cycle were at different temperatures.

> with sander.MPI, can i simulate step2 successfully? although it is not
> necessary.

in step 2 vacuum the transition is between a chargeless molecule and
'nothing' and the concept of an empty system is hard to setup in the
sander.MPI framework. If you are not convinced that this step can be
ignored, you could repeat your transformation using dummy atoms and should
get the same result. You would have to repeat the complete cycle, though,
since doing the steps with dummy atoms changes all substep results (but,
hopefully, not their sum).


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

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Received on Wed Feb 23 2011 - 01:00:05 PST
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