[gmx-users] (no subject)

cilpa at users.csc.fi cilpa at users.csc.fi
Wed Feb 13 14:36:31 CET 2008

Hi all,
i 'm a beginner in molecular dynamics. I was doing the tutorial of md
group, hydration free energy of toluene :

 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
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
Would you have any idea what could be the problem?
Helsinki university

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