AMBER: Dummy atoms: Changing the source code

From: Ilyas Yildirim <>
Date: Thu, 3 Mar 2005 19:24:03 -0500 (EST)

Dear David Case,

In my prev. emails, I was asking why AMBER does not let us use dummy
atoms in the initial state when k is not equal to 1 (pp.134, note #2). And
as far as I understand, the reason lies at the parameter function chosen
in Eq. # 5 (pp.133). When I plot the function, (1-lambda)^k, it seems
that when we have dummy atoms at the initial state, the transformation
will be sharp. It is not as gradual as it is when we have dummy atoms at
the final state.

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
  - Department of Chemisty       -                              -
  - University of Rochester      -                              -
  - Hutchison Hall, # B10        -                              -
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) -
  -                     -
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Received on Fri Mar 04 2005 - 00:53:00 PST
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