[gmx-users] free energy and ions
Alan Wilter Sousa da Silva
alan at biof.ufrj.br
Wed Nov 27 20:04:59 CET 2002
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
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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