> Have you seen any information to suggest that this is actually a > non-trivial concern? That is, given static point charges, an empirical > LJ force, short cutoffs, etc., do you believe that the application of > nose-hoover, berendsen, or even the arbitrary velocity rescaling > significantly degrades the quality of the obtained dynamics?
1) I think there's an important distinction to be made here between accuracy and physical validity. If you use a thermostat, then the dynamic properties you obtain for the system will be different than the properties obtained without the thermostat, independent of what model you choose. So, I don't know that it's that useful to ask whether the differences from the true system due to thermostat are large compared to the differences due to the choice of model -- the results are going to be dependent on the thermostat, so the field has chosen a standard definition of the dynamics, one that most resembles the actual physical system (where there isn't temperature rescaling every 2 fs or a piston coupled to a 10 nm cube of water, etc). 2) If one uses the Berendsen thermostat, then statistical mechanics of canonical ensembles will not strictly apply, and one can't use many of the results one would like to (or, are using already incorrectly). One can do physics-based simulation of molecular models, or one can do non-physics-based simulations of molecular models. In many cases, the non-physics-based results will be statistically indistinguishable from the physics based results. But why bother with an uncontrolled approximation when you don't -have- to use one? It just adds another chance that what one simulates is not reproducible or reliable, and heaven knows that simulation currently has enough of those already. It's like building a tower out of blocks, and each uncontrolled approximation, no matter how small, is a bit of unevenness in the block. If you have just one wobbly block, you can stand on it pretty well -- you know the limits of the approximation, you can get a pretty good sense of what's going on with the system. Once there's a large number of wobbly blocks, though -- good luck standing on top of it and trying to build good science. As simulations get larger and more complicated, they are built out of more and more blocks, and we need to make sure we're paying careful attention to how well they all fit together. Best, Michael Shirts Research Fellow Columbia University Department of Chemistry _______________________________________________ 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