Re: AMBER: Dummy atoms: Changing the source code

From: Julien Michel <>
Date: Fri, 4 Mar 2005 09:44:31 +0000


> So, we were thinking that if we use a parameter function,
> tanh[k(2lambda-1)], such that the Eq. 5 becomes,
> V(lambda)= tanh[k(2lambda-1)]*V0 + {1 - tanh[k(2lambda-1)]}*V1
> the problem might be solved. When we plot the function tanh[k(2lambda-1)],
> we see that the initial and the final transformations look gradual. So, we
> were wondering how we can change the AMBER code such that we can use this
> new function rather the old one. Do we have to change just the
> thermo_int.f file, or something else too? Thanks in advance.
> Best regards,
> Ilyas Yildirim

    Which values of k would you advocate then ? In principle, one of the
potential should be zero at the end state, which you don't get if you don't
set k to a high value. K would have to be large (more than 10) to extinguish
the LJ of V1 at a lambda value close to 1. Furthermore, if you use this
functional form, you will simply see that that your Hamiltonian is more or
less constant until the region of lambda 0.5 where it is rapidly changing,
thus your perturbation will just be harder to accomplish at lambda 0.5 instead
of 0.0 or 1.0.
  You might want to read some papers on soft-core if you are interested in
creating/destroying atoms in a free energy simulation (see J.Chem.Phys
,100,12,9025 for example).

Julien Michel
University of Southampton
Department of Chemistry
Dr J. W. Essex group
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Received on Fri Mar 04 2005 - 09:53:00 PST
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