Dear all, A couple of weeks ago i reported a problem I encountered with free energy calculations. I've figured out by now what the problem was (a mistake in the input, as usual ;) ... however, while searching for the solution i made a couple of observations that might be interesting for others (including the developers). they are listed below.
1) the result of the electrostatic contribution does depend on what soft core parameter p i use. If I use p=1 the results are wrong (10-15 kJ/mol off the literature value), with p=2 i can reproduce literature values (+/- 1 kJ/moil). It might be that with p=1 it simply takes much longer to converge, but then in both cases the error-bars look quite reasonable, and also from visual inspection of dG(t) the results seem to have converged. 2) i get the same results when using md+NH thermostate with two thermostates, or langevin dynamics (sd), the error bars are somewhat larger with sd though. 3) i get the same results when doing slectrostatics and VdW seperately or in one go, (provided i use p=2). system/protocols: 462 TIP3P water in a cubic box, 12 A cut-off, PME with nk=32 or 64. free energy from trapecoidal integration of <dU/dlam> from 21 windows, at least 100 ps per window, sc_alpha = 0.5-2.5, sc_p= 1 or 2, sc_sigma=0.3. error-bars taken to be the RMSD of dGs obtained from 10ps/window subsets. for what its worth ... mic ____________________________________________________________________________________ Never Miss an Email Stay connected with Yahoo! Mail on your mobile. Get started! http://mobile.yahoo.com/services?promote=mail _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
