Any progress on this? (I note a prior discussion of the idea for a "g_strain" program, under the subject line of "How to print out vdw-14 energy terms for each pair in minimization?") I have actually defined energygrps for each charge group in each residue, via a script (which I will forward if desired), via which (along with gmxdump) it appears possible to get out coulomb and lennard-jones interactions (subdivided into 1-4 bonded and short-range) between said energy groups - but gmxdump indicates that the bond energy terms are still only present for the entire system. I'd like to do something like putting a number proportional to the total energies (would "Energy" or "Sum Energy" - for the final stage in a minimization - be more appropriate?) into the temperature field of a PDB file. (I have also considered the possibility of doing this with forces - I will try outputting force terms seperately via mdrun -sepdvdl with my next minimization, and will use mdrun -rerun -sepdvdl on earlier trajectory files if this is helpful - but the summation of forces (e.g., an atom under vdw pressure from "above" and "below") would appear likely to cancel out information of interest.)
Thanks, -Allen P.S. In regard to my earlier thoughts on FFTW improvements - will try to work on at some point, but am mainly working on Linux boxes at the moment so this is less of a concern. I have also discovered exactly how fast GROMACS is at doing minimization of even a well-solvated protein, which also decreases this priority; very nice job, guys! > [gmx-users] how to calculate internal energy for energygroups? > > Marc Baaden [4]baaden at smplinux.de > Tue Jan 23 14:40:38 CET 2007 > > * Previous message: [5][gmx-users] how to calculate internal energy > for energygroups? > * Next message: [6][gmx-users] Error using -demux flag in trjcat > (development version) > * Messages sorted by: [7][ date ] [8][ thread ] [9][ subject ] [10][ > author ] > _________________________________________________________________ > >>>> David van der Spoel said: > >> Maybe we should go back one step. The reason this is not implemented is > >> because we thought it would be unnecessary. In addition, if you would do > >> it per residue how would you categorize e.g. the dihedral terms with one > >> atom in one residue and three atoms in another? Of course you can define > >> something, but what does it mean? > > >Ok, first a general comment: > >I have used this in the past and found that the sum of all bonded energy >terms for a given residue or for a subpart of a molecule is a good measure >for the internal strain of that entity. Of course one may want to normalize >this depending on what one wants to compare (per residue / per atom / per >domain ...). > >I agree that the part of this entity that is connected to the rest of the >molecule is ambiguous. I usually disregard all bonded terms that are not >entirely contained within the selected atoms (the logic being that you can >always make your selection bigger if you want). > >The problem that there might be with the way g_energy works at the moment >is that I think g_energy tries to split the energy in parts so that by >summing the parts you obtain the total sum again. That is you can't put >an atom in two selections at the same time. > > >For the specific case I want to use this now: > >In the system we are simulating we observe a specific pattern of contacts vs >the residues of the macromolecule. We think that the origin for this lies in >the balance of the different force-field terms for each residue. So I would >like to make a plot of the interaction energies for each residue with the rest >of the system split into electrostatic, van der Waals and bond/angle/dihedral >contributions to see what the major contributions are and whether the pattern >varies from residue to residue. > >I hope this does make sense and provides at least one reason to implement >such a procedure. > >Marc >-- > Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris > mailto:[11]baaden at smplinux.de - [12]http://www.baaden.ibpc.fr > FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 -- Allen Smith http://cesario.rutgers.edu/easmith/ February 1, 2003 Space Shuttle Columbia Ad Astra Per Aspera To The Stars Through Asperity _______________________________________________ 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