Hi Gideon, If the binding is relatively weak and the force field parameters are good enough that should be feasible. See e.g., Biophys J. 2005 August; 89(2): 768–781. However, in other cases this is more challenging. This is discussed in details for simulations of a Zinc binding protein in Phys Chem Chem Phys. 2009 Feb 14; 11(6): 975-83
Good luck, Ran ------------------------------------------------ Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden +46 480 446 290 Telephone +46 76 207 8763 Mobile ran.fried...@lnu.se http://lnu.se/research-groups/computational-chemistry-and-biochemistry-group?l=en ------------------------------------------------ ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of גדעון לפידות [glapid...@gmail.com] Sent: 30 November 2010 10:45 To: gmx-users@gromacs.org Subject: [gmx-users] Claculating Equilibrium constants Hello all, I have a protein bound to ions. is there a way to calculate the Kd of the bound ion in Gromaces so I can compare it to experimental Kd? Thanks, Gideon
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