Hi, 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 e-mail.
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. Thanks, David Mobley On Feb 11, 2008 5:14 AM, <[EMAIL PROTECTED]> 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 > > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php