[gmx-users] Re: free energy calculation

David Mobley dmobley at maxwell.compbio.ucsf.edu
Tue Feb 12 05:40:36 CET 2008


I am traveling and don't have time to answer this now, nor am I
responsible for the tutorial you mention. I also only usually answer
questions like this on the gromacs users list, not in my personal

I suggest you direct your e-mail to the Gromacs users list (which I am
ccing on this) and get help from someone else on there, or i will be
able to attend to it (in that forum) in a few days.

David Mobley

On Feb 11, 2008 5:14 AM,  <cilpa at users.csc.fi> wrote:
> Dear david,
> i 'm a beginner in molecular dynamics. I was doing the tutorial of md
> group, hydration free energy of toluene :
> http://md.chem.rug.nl/education/Free-Energy_Course/2.hydration-fe.html
>  i have some problems regarding the calculation of toluene in water. the
> thing is that in the examples files equ-10.00.mdp and data-10.00.mdp no
> sc-power were mentioned and doing the calculation the error files
> mentioned about sc-power must be >0 so i added this line sc-power=1 to
> those files. Analyzing the dgdl.xvg files the estimate error(err. est.)
> is about 5.79.... for each lambda value studied while the mutation of
> toluene to dummy in vacuo gave really reasonable rms of about 10E-5.
> Combining the integration value of the plot in water and vacuo did not
> give me the right solvation free energy value (compare to experimental
> one).
> i assumed that this is the free calculation in water which is problematic.
> I tried to play with sc-power and sc-alpha but still even if those
> parameters seem to influence a lot on the energy no real improvement are
> visible.
> Would you have any idea what could be the problem?
> geraldine
> Helsinki university

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