hello all.
i am trying to trying to write an analysis program that takes advantage of the gromacs utilities/structures. for my analysis i need to identify each type of interaction in the potential energy function and the atoms involved in each equivalent interaction of the given type. for example, for each different type of bond angle, i would like to identify each triple of bonded atoms forming the given type of bond angle. also i would like to be able to identify each pair of atoms - one of type A and one of type B - that interact through a nonbonded (lennard-jones type) A-B interaction. i would like to use something like "read_tps_conf" to read a tpr file and then extract these lists of pairs, triples, etc. from the interaction list in the topology data structure. however, after spending some time fiddling around with interaction list data structures such as idef and ilist, it is still not obvious to me how to extract this information. after reading through types/idef.h, it seems that the information i need is stored in these structures, but i still don't understand how they are used. is there a relatively easy way to get these lists of interactions for each interaction type out of the tpr file? and if so, can someone please enlighten me as to how this is done? of course this information can be obtained from the .top file and i have started writing my own utility for extracting this information directly from the .top file. however, if there is a clean way to extract the information from the .tpr file using gromacs utilities that are already written, that would be a big help. thanks to anyone who can help me out here. will noid _______________________________________________ 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
