On Thu, 1 Jun 2017 14:16:38 -0400
Sumudu Leelananda <sumudu.leelananda.gmail.com> wrote:
> Dear all
>
> I'm doing thermodynamic integration to find the free energy of Ca
> binding to my protein. The simulations run without issues when I use
> pmemd. I use a multisite Ca ion model.
Is this something like this?
http://septlab.engin.umich.edu/multisite-ions.html
> Previously for pmemd timask1 =90 and timask2 = 91 were used for this
> step (two copies of the multisite Ca ion).
This does not look like a proper mask to me. What are those numbers
referring to and what is the end state? When you say binding free
energy (and restraints) I would expect that you would want to carry out
an "absolute" (standard) free energy calculation in which case your end
state is "nothing" i.e. you want to dec
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Received on Thu Jun 01 2017 - 12:00:02 PDT
