[gmx-users] Charmm foce field and free energy

Eudes Fileti fileti at gmail.com
Sun Jul 8 02:47:44 CEST 2012

Dear all,
I'm trying to reproduce the hydration free energy of the methanol using
the CHARMM force field. However I am getting a value considerably
lower than the experimental: 17 kJ mol-1 (the experimental value is 21
kJ mol-1).

Am I forgetting some technicality related to the force field?
I using a detailed thermodynamic integration procedure, where I decouple
Couloumb and van der Waals interactions separately, at lambda
intervals of 0.04.
I'm using sd integrator and softcore to decouple van der Waals interactions.
Other details:
NPT, box with 1000 TIP3P water molecules and one methanol molecule,
400ps per window.

In a general review I noticed that is not easy to obtain good
accuracies in this property.
For example, the original paper (J Comput Chem 29: 2543, 2008), is reported a
overestimated value of 23.9 kJ mol-1. In J Phys Chem B 110: 17616,
2006, Hess got a underestimated result
by 2 kJ mol-1. Shits reported a value of 18.87 kJ mol-1 in J Chem Phys
122: 134508, 2005.
These inexact values is inherent to the models or there was any way to improve
the accuracy through the protocol used?

Eudes Eterno Fileti
Instituto de Ciência e Tecnologia da UNIFESP
Rua Talim, 330, São José dos Campos - SP
Tel.: (12) 3309-9573
Página: sites.google.com/site/fileti/

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