Re: [AMBER] How to simulate hydration free energy with thermodynamic integration?

From: <>
Date: Fri, 18 Feb 2011 10:11:31 -0500 (EST)


> then modify LENNARD_JONES_ACOEF and LENNARD_JONES_BCOEF within benwv.prm
> file to 0.00.

I would recommend using dummy atoms instead of changing vdW-parameters in
the prmtop file,if you really want to use linear mixing (aka non-soft
core) for your calculation, which you probably dont.

> (1) How to create simulation files for the LJ step? in the simulation,
> whether use softcore or not?

I recommend using softcore potentials, which also makes the setup easier.
You try to simulate a benzene molecule disappearing from a water box,
therefore your two states should be solvated benzene and an empty water
box. Make sure that the same number and coordinates of water molecules are
used for V0 and V1.

> (2) For the non-hydrated benzene, do we also use periodic boundary
> conditions?

No, disappearing benzene would happen in vacuum, but the vdW step for that
need not be actually done, since all internal energies of a disappearing
molecule are already considered correctly, meaning that dVdl for
disappearing benzene is always zero. However, the charge removal step in
vacuum (benzene to chargeless benzene) would need to be done if you use
the two-step setup you describe.

Kind Regards,


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

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Received on Fri Feb 18 2011 - 07:30:02 PST
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