Maik, > Assume, you take the interconversion of ethane to methanol in solvent in > one step. > You sample hardcore at 11 evenly spaced lambda values for, lets say, 2 > ns each. > You get the dG/dl mean from every run and integrate via simpson to get a > total DG.
Hold on, if you are doing this with hardcore, there is a singularity in dG/dlambda. It won't be numerically integrable so whatever you compute will be in error. See my recent JCP paper that I referred you to before. I think if you are using hardcore, you *have* to use slow growth and the Jarzynski or Crooks expressions, or do some sort of polynomial fit to the singularity in dG/dlambda and integrate the polynomial. Integrating dG/dlambda directly will simply fail since you can't numerically integrate a singularity. If you're using softcore, you have more options, and simple numerical integration can work. For what it's worth, too, a delta_lambda of 0.02 is insanely fast "slow growth". David _______________________________________________ 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
