This is my understanding. Please correct me if I'm wrong.
It isn't analytically zero at lambda=0 for icfe=1 (icfe=2
wasn't available in Amber 8).
The mixing function goes to zero at lambda=1 for higher values
of klambda, but the potential being mixed isn't nicely behaved
-- it diverges at lambda=1. What matters is the combination
of the two functions.
If you look at David Case's example
(
http://amber.scripps.edu/tutorial/shirts/index.html), a
favorable combination of cut values and klambda can, indeed,
converge to zero at lambda=1, but they don't necessarily.
I don't think I -need- the DV/DL to go to zero at lambda=1.
Merely being finite is probably ok (if someone who's done more
math on this disagrees, I'd gladly hear their arguments). I
think I just need the value to be finite and to know what the
value is.
:-) lachele
>I am not sure how this works with icfe=1, but when I set
icfe=2, for
>lambda=0 and lambda=1, the dv/dl values are not printed out.
They are
>analytically zero. When I run with lambda=0.05 or
lambda=0.95, I am
>getting dv/dl values, but they are close to zero. I am doing
a dummy to
>hydrogen and hydrogen to dummy transformations in the TI
calculation. So,
>I am guessing that the same thing happens with icfe=1 when
lambda=1,
>because analytically it is zero.
>
>On Fri, 10 Mar 2006, B. Lachele Foley wrote:
>
>> I've done van der Waals perturbation in Amber 8 and Amber 9.
>> My issue (below) happens in both. I want to know if it can
>> change for Amber 9.
>>
>> The context, here, is disappearing atoms in an explicit box of
>> water by first turning off charges and then by turning off the
>> van der Waals.
>>
>> When I run the charge perturbation, I get DV/DL values printed
>> in the output file for all values of clambda.
>>
>> When I run a vdW perturbation, I get DV/DL values printed in
>> the output file for all values of clambda except 1. There
>> should be a value at 1, even if it's zero. When I say not
>> printed, I mean that "grep DV\/DL blah_1.000.o" yields nada.
>> Do you know why the values aren't printed? Can they be
>> printed? I'm using klambda=6, if that's important.
>>
>> You'd never notice this with quadrature. For my systems,
>> though, having endpoints seems to improve accuracy.
>>
>> :-) Lachele
>> B. Lachele Foley, PhD, '02
>> Assistant Research Scientist
>> Complex Carbohydrate Research Center, UGA
>> 706-542-0263
>> lfoley.uga.edu
>>
>>
>
>--
> 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/ -
> ---------------------------------------------------------------
>
B. Lachele Foley, PhD, '02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
706-542-0263
lfoley.uga.edu
Received on Wed Apr 05 2006 - 23:49:40 PDT
