[gmx-users] (no subject)

Maik Goette mgoette at mpi-bpc.mpg.de
Wed Feb 13 17:19:58 CET 2008


First of all: You can be quite happy, if anyone reads a "no subject" mail.
sc-power seems to be set to zero in the newer version, in contrast to 
the old ones, where it was 1 by default.
Therefore GROMACS complains. 1 is the value, you should use.
I don't know the tutorial, but if you use exactly the files given there 
(and add sc-power = 1), you should get values, which are close to the 
experimental one (I guess, cause a tutorial won't make sense, if the 
files don't yield the desired value).

Sorry, but more help is hard to give with so few information.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

cilpa at users.csc.fi wrote:
> Hi all,
> 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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