# Re: AMBER: Dummy atoms: Changing the source code

From: Ilyas Yildirim <yildirim.pas.rochester.edu>
Date: Fri, 4 Mar 2005 21:56:34 -0500 (EST)

Hi,

The functional form of the parameter function I want to use is
(1+tanh(k*(2x-1)))/2. Here k is 3,4,5... If I use k=3 or k=4, the
function is pretty smooth. Initially it is zero and gradually increases
till it gradually becomes 1 at x=1. I dont see any reason why it should
not work. If we want to use a function which will let us use the dummy
atoms in the molecules, I cannot think of any other function than this one.

Best,

On Fri, 4 Mar 2005, Julien Michel wrote:

> Hi,
>
> > 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).
>
> Regards,
> ----
> Julien Michel
> University of Southampton
> Department of Chemistry
> Dr J. W. Essex group
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>

```--
Ilyas Yildirim
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Received on Sat Mar 05 2005 - 03:53:02 PST
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