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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
*

*> -----------------------------------------------------------------------
*

*> The AMBER Mail Reflector
*

*> To post, send mail to amber.scripps.edu
*

*> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.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:

-- Ilyas Yildirim --------------------------------------------------------------- - Department of Chemisty - - - University of Rochester - - - Hutchison Hall, # B10 - - - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) - - http://www.pas.rochester.edu/~yildirim/ - --------------------------------------------------------------- ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Sat Mar 05 2005 - 03:53:02 PST

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