I had a look at the manual for the new amber11 and the wording for the ifsc
options is clear enough that I now feel like I understand what is going on.
Problems over, and sorry to bother all of the 1 million people who will find
this post through google in the years to come.
On Mon, May 3, 2010 at 1:08 PM, Josh Berryman <
the.real.josh.berryman.gmail.com> wrote:
> Hello Team, and thanks in advance for helping. I am trying to run a TI
> calculation in which a box of water disappears to nothing using the softcore
> potential, and icfe = 0, as mentioned in the amber 10 manual sec 4.1 page
> 107. This may seem perverse, but the functionality *is* advertised as being
> there.
>
> Where is the DV/DL value? SC_DERIV appears always to be zero in the output
> and DV/DL is not printed. This matches the output for test case
> 'test/softcore/pert2nil/mdout.save' so I assume that there is no problem
> with the program or with my input file, only my limited understanding.
>
> Am I supposed to differentiate the Hamiltonian in (Steinbrecher, Mobley,
> Case JCP 2007) with respect to lambda myself? What about 1-4 interactions
> etc - will the derivative with respect to lambda be the same for these? I
> am worried that I have not got the right end of the stick here.
>
> Josh
>
>
>
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Received on Mon May 03 2010 - 11:00:04 PDT
