> -----Ursprüngliche Nachricht----- > Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] Im Auftrag von Andrew DeYoung > Gesendet: Samstag, 14. Juli 2012 18:56 > An: gmx-users@gromacs.org > Betreff: [gmx-users] Re: Conceptual question: Why are MD production > simulations usually run in the NVT ensemble? > > Hi Justin, > > Thanks so much for your time. > > You make a very good point about NPT. My field (although I am only a second- > year graduate student) is physical chemistry, and I am ignorant, unfortunately, > of biochemical literature. > > In physical chemistry, it seems that people almost always use NVT for > production simulations, but I am not sure why, because just as in biochemical lab > experiments, I would expect NPT to be more realistic -- chemicals (whether it is > a pure liquid, like in "my" field, or a solvated biomolecule, like in "your" field) are > usually exposed to atmospheric pressure in experiments. In experiments, the > volume is usually not fixed, I think. So it makes sense you say that biochemical > simulations are typically performed in NPT. I don't know why physical chemistry > experiments on, and simulations of, liquids would be any different. >
Hi, I completely understand your question, because it also came up to me. As Justin mentioned, NpT simulations are the common situation for biophysical processes in cells, because it is their native environment. The minimum of the Gibb's free energy G=H+pV determines the system state. Assuming you are performing an equilibrium MD, G is a constant of motion. Now the task of the integrator including the thermostat and barostat is to keep G constant. If you perform an NVT simulation you have no control over G but only the Helmholtz free energy H=U-TS. Hence if you are interested in a certain state of the system like folding of a protein or free energies, which depend on G you have to simulate the corresponding ensemble. If you want to study thermodynamic properties such as density, conductivity, diffusion, the choice of the ensemble depends on other reasons. If you want to study the density, an NVT simulation is not useful, because you set the density as input parameter. However, if you are able to extract the desired data from an NVT ensemble, it is preferable to an NpT simulation, because you do not have to assure that the barostat couples correctly and the sampling is sufficient to have no bias from the barostat. This is especially important if you are studying new compounds, where the system is not well study such that a proper adjustment of the barostat parameters is difficult. Sometimes it is also difficult to sample canonically in an NpT ensemble, if the simulation time is short, the system is small or the virial theorems are not sufficiently fulfilled for other reasons. The common protocol to equilibrate in NpT and perform a production run in NVT is finally related to Justin's comment regarding the parameterization. An equilibration of the system can only be achieved, if the system is allowed to get into the corresponding state given by the force field. If you would have a "perfect" force field, you could also skip the NpT equilibration, because with the knowledge of the experimental density you could setup your system in the correct state and sample in an NVT ensemble. At the end in the NVT production run you only have to assure that you sample long enough to obtain a reliable average of dynamic properties, like diffusion or conductivity, such that they are not biased by the thermostat. This is my opinion to this matter and I hope it helps, but please correct my, if I am wrong. /Flo > I guess then this could be an issue of the field? Are there chemists or physicists > reading this that can please provide advice? > > Best wishes, > > 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 -- 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
