>>> 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:[EMAIL PROTECTED] - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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