[gmx-users] Calculate ion disasociation constant

[Mark Abraham]

On 7/12/2010 6:34 PM, גדעון לפידות wrote:
> Hi all,
> Does anyone know of way I can use Gromacs to calculate the 
> disasociation constant of a calcium ion held by two loops in a protein 
> in water simulation? my starting point was a pdb file of the protein 
> with the bound ions in place. Eventually I would like to evaluate the 
> time constant (meaning, on average, how long it would take the ions to 
> leave the protien)

All this requires that you calculate an accurate free energy of 
dissociation. You will not have enough computer time to watch multiple 
association-disassociation events in a simulation. Maybe the pull code 
in GROMACS can help with this, but I really know nothing about the pull 
code.

Mark