[gmx-users] free energy and ions

Alan Wilter Sousa da Silva alan at biof.ufrj.br
Wed Nov 27 20:04:59 CET 2002

Hi List,

	I'm trying to calculate binding free energy of a complex
substrate/protein using linear approximation (Hansson & Aqvist, Protein
Eng. 1995, 8, 1137-1144).
	Both protein and substrate are charged, so I used ions and PME.
However, observing dynamics (1 ns) I can see that for the complex ions
keep around substrate during whole simulation, while MD of the only
substrate in water a ion start close from it but after 100 ps it goes
	Using g_energy I could note a great difference when analyzing the
first 100 ps (for both simulation) to the last 100ps, all due to the
interaction between ions and substrate.
	In other words: Coul-SR:Substrate-CL- energy for complex
oscillates with time (never zero) while Coul-SR:Substrate-CL- energy for
substrate goes to zero in only 200 ps and there it remains.
	I emphasized Coul-SR:Substrato-CL- because it change completely my
energy binding estimations.
	With substrates not charged I got really good results (compared to
experimental values).

	How can I keep a coherence for analysis?
	How bad would it be if I discard ions and rerun both simulation?
	Should I run more 1 or 2 ns and so get a more reliable statistic?

Many thanks in advance for any suggestion,


Alan Wilter S. da Silva
 Laboratório de Física Biológica
  Instituto de Biofísica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil

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