Thanks for your comments! Berk Hess wrote:
> One "obvious" problem is that using two thermostats is incorrect. > In this way the com of the water with respect to the com of the rest > will not be sampled correctly (both are fixed). I am not sure I understand what you mean, is the COM reset for each temperature group seperately or not ?? (I used nstcomm = 100) ... when the systems are still interacting, i.e., when lambe < 1 I wouldn't expext this to be a problem, while when the water is completely de-coupled (lambda=1) then I actually NEED to use two thermostates plus a finite nstcomm, since otherwise I might end up with a water thats either much too "hot" or too "cold", or a tumbling ice-cube ... > The solution is using the sd integrator. There must be a way to do that with a normal verlet algorithm or the like ... the sd integrator, i.e. the Langevin dynamics, was meant to be used with implicit solvent, after all. There is this friction term that's meant to mimic the effect of the explicit water, and even if you let the friction constant zeta be very large, i.e., if you do away with the friction term, you just end up with a primitive kind of thermostate, and i can't see a reason why this should be any better than Nose Hoover !? > Another issue is that since water is strongly hydrogen bonding > and the hydrogen bond interaction is rapidly soft-cored, > you probably need much closer spaced lambda point at lambda=0 > (i.e. use an inhomogeneous spacing). that would mean to forgo one of the advantages of softcore potentials altogether, since this is exactly why we use them: to spare ourselves the extensive sampling required when approaching lambda=1 (where the interactions between particle and the rest approach zero, and dA/dlambda diverges) I've simulated the very same system in CHARMM, with soft core potentials plus NH thermostate, and 21 equally spaced windows, and got perfectly reasonable results. can it be that the small LJ interaction parameters that CHARMM gives the TIP3P water hydrogens (for reasons related to a completely different problem, and in fact irrelevant for the resulting (free) energies) makes all the difference ?? > There could be other issues, but one would only find those > after studying the results in detail. that's what i am doing at the moment. cheers, michael ____________________________________________________________________________________ Need a quick answer? Get one in minutes from people who know. Ask your question on www.Answers.yahoo.com _______________________________________________ gmx-users mailing list [email protected] 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
