[gmx-users] Re: Solvation Free Energy calculation (g_bar)
Justin A. Lemkul
jalemkul at vt.edu
Mon Jun 18 22:14:45 CEST 2012
On 6/18/12 3:05 PM, Daniel wrote:
> Hi Justin,
> Thank you for your reply. I see what you mean, but the problem is when I use
> the approach you mentioned (adding the DGs) my result is far from the
> experimental one, whereas when I choose the first one (which violate the
> Second law) my result is quite good, except for the error estimation and the
> warning, It seems that it makes an important difference the way the g_bar is
> applied, considering my simulations are right.
> Now I'm trying to increase the number of lambdas in the region where the
> Second law has been violated in an attempt to solve this issue, Anyway, I'm
> stil not sure if my procedure is correct and why I'm getting such a
> difference when applying the g_bar in these two ways.
The warnings you are receiving arise because you're concatenating dissimilar
data sets (one where LJ are being decoupled, and one where Coulombic
interactions are being decoupled) and expecting the result to make sense. It is
possible to (de)couple both LJ and Coulombic terms simultaneously, but I have
never done this myself; I have always relied on a two-state (de)coupling procedure.
As to the quality of the result, I can't comment on that because I don't know
what you're working with. The quality of the result is dependent upon the
quality of the topology, so if you're trying to develop new parameters for a
molecule, you may need to reconsider how the parameters were derived.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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