Hi, Thanks for your time. Based on Justin's and Florian's responses, it seems that the choice of whether to do production simulations in NpT or NVT depends on what you're studying. Does the following seem like a reasonable summary of the discussion:
-- In biophysics, lab experiments are almost always performed at constant pressure (i.e., atmospheric pressure), so NpT is the natural choice. Moreover, in biophysics, people are often interested in particular system states, like the folding of a protein. These states depend on free energies, which in turn depend on the Gibbs free energy G. This necessitates the use of the NpT ensemble because it is the only ensemble (I guess?) that allows control over G. -- In physical chemistry studies of liquids, I speculate that lab experiments are still almost always performed at constant pressure. However, in these types of studies, people are less frequently interested in particular system states; hence calculation of free energies are typically not necessary. But just because calculation of free energies is not necessary does not mean that NpT cannot be used. Nevertheless, NVT is preferable in that it avoids the use of a barostat, which can give rise to artifacts and whose parameters are difficult to set for new compounds. A fellow student put forth one more possible distinction between biophysics and physical chemistry. He pointed out that in biophysics, one often studies macromolecules like proteins, which undergo significant structural changes and hence undergo large changes in volume during the simulation; hence NVT should not be used. In contrast, in physical chemistry, one is more often interested in small molecules. Small molecules do not undergo large structural changes, so the system volume is expected to vary very little during the simulation; hence NVT is permissible. Also, NVT is _perhaps_ slightly less computationally expensive than NpT, so NVT should be used when it is permissible (i.e., when folding does not occur and when calculation of free energies is not needed). Do you agree with this reasoning? Do you think that protein folding leads to large changes in system volume, whereas in liquids the system volume is not expected to change much? Thanks so much! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists