What exactly do you need comments on? Your analysis looks right to
me.
Cheers,
Hannes.
On Tue, 25 Nov 2014 00:10:22 +0800
sun <sun.ntnu.edu.tw> wrote:
> Hi,
>
> We are learning TIcomputation using pmemd. One thing we noticed is
> that,
>
> we mutated ligand0 (50 atoms) to ligand1(52 atoms) in solution with
> 30 common atoms (# of softcore atoms are 20 and 22, respectively,
> certainly). The computed DeltaG was -20 kcal/mol.
>
> When we reduced # of common atoms to a few atoms, the computation
> gave DeltaG of -4 kcal/mol.
>
> I think this is not because of sampling issue but about how DV/DL is
> counted. (in the manual, it said only non-bonded interactions of soft
> core atoms contributes to DV/DL, not bonded interaction).
>
> Considering Delta G is a state function, at the first look, DeltaG
> should be the same even # of common atoms is reduced.
>
> My guess is that this "effect" will be cancelled out in the
> thermodynamic cycle.
>
> along this thinking, it seems that, suppose we want to reproduce
> sander's DeltaG using pmemd, we need to make the right choice of
> common atoms. (I am still thinking about this!)
>
> comments are welcome and appreciated.
>
> thanks.
>
> Ying-chieh
>
>
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Received on Mon Nov 24 2014 - 08:30:04 PST
