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 _______________________________________________ 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
