I would not use NO as a type name - it will likely collide with an
existing type in use. DU (for dummy) is a traditional name for this sort
of purpose. Hopefully someone will answer the perturb-to-nothing
question in more detail, but experimentation is cheap in the meantime.
Here is some early ion perturbation work that might be of interest.
Ion-Induced Stabilization of the G-DNA Quadruplex: Free Energy
Perturbation Studies. W.S. Ross and C.C. Hardin
Journal of the American Chemical Society 116, 6070 (1994).
Bill
On 4/17/17 1:05 AM, JinpengYang wrote:
> Dear Professor:
>
> When I calculate the solvation free energy of Ni2+ in water using sander using two-step thermodynamic integration(TI) method.The first step was perturbing nothing to the metal atom Ni(with no charge) in water using the soft-core potential. Then the problem is how I setup the model of nothing in water.
>
> If I addAtomType NO(with zero MASS,zero charge,zero Non-bonded),whether the atomtype No means nothing?
>
> Your any reply will help me a lot.Thanks in advance.
>
>
> --
>
>
> All the regards,
>
> Jinpeng Yang
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Received on Mon Apr 17 2017 - 02:00:02 PDT
