2012/11/3 Justin Lemkul <[email protected]>: > > > On 11/2/12 11:35 AM, Hanne Antila wrote: >> >> Dear experts, >> >> This question has been asked several times before but so far it >> remains unanswered. >> >> I would like to calculate the total energy (kinetic plus potential) >> for a group of molecules. In my case, I would like to look at certain >> water molecules. So far, I know that I can get the kinetic energy from >> g_traj, and some of the potential energy components by defining energy >> groups and using g_energy (Coul-SR, Coul-14, LJ-SR, LJ-14). It is >> unclear for me whether this is really all the components I need? Also, > > > I'll repeat one of the comments that has often been made before - of what > use is this? One can pick a given configuration of water and calculate its > energy, but the relevance of these configurations, in isolation, is very > debatable. There will be no 1-4 terms for water molecules, since they only > have 3 atoms. In theory, one would also need bond and angle terms for these > molecules to fully describe the internal energy, but if using a rigid model > (likely), then these energies will not exist.
The reason I'm asking is that I'm trying to estimate the entropy of water molecules near a DNA strand. I'm more or less following what has been done in this article: http://pubs.acs.org/doi/abs/10.1021/jp061588k. You are right, I don't need the internal terms. I mentioned the 1-4 terms to illustrate what one can get out by defining energy groups. > > >> is there some technical reason why one doesn't get the average group >> kinetic/potential/total energy directly from g_energy by defining >> energy groups? >> > > The size of the .edr file would explode. Since one can already get kinetic > energy for a group using g_traj with a .trr file, there is no point to the > redundancy. I also recall reading about technical problems with doing this > (especially in decomposing bonded terms and pairwise energies), but I can't > point you directly to that post. Yes, I suspected something like this. It would be convenient if there would be some more freedom of choice for the energy terms, but I can see why this might be laborious to execute. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== Thank you for the help! -Hanne > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
