hello again.
thank you very much to drs. Groenhof, Abraham, and van der Spoel. i
greatly appreciate your time and help. dr. Groenhof's email and the
pdf file that he linked were particularly helpful. i would suggest
that the pdf file would be a great addition to the gromacs wiki.
with your help, i now can access the lists of interacting pairs,
triples, etc. for each type of bonded interaction. however, i am
still having difficulty accessing the lists for the nonbonded
interactions. as the comments in types/idef.h suggests,
idef.il[F_LJ].nr=0, so the lists of pairs of nonbonded interactions
are not stored there.
dr. van der Spoel mentioned that the nonbonded interactions are
organized as a matrix at the beginning of the idef. i can see that
the first interaction types (and their corresponding sets of iparams
and functypes) correspond to these nonbonded interactions. however, i
do not understand how to access the information that must be stored in
this interaction matrix. (i don't quite understand where this
interaction matrix is in the idef structure either. sometimes these c
structures are a little bewildering to me - fortran is my native
programming language.) if someone could indicate how to access these
lists of nonbonded pairs that would be greatly appreciated.
thanks again for your time and help.
will noid
Message: 1
Date: Tue, 04 Sep 2007 08:37:11 +0200
From: David van der Spoel <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] interaction lists in idef.h
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
[EMAIL PROTECTED] wrote:
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.
try checking out similar utilities, like src/tools/mk_angndx.c
you may even use that to generate simpler index file as input for your
tools.
for nonbonded an interaction matrix is stored at the beginning of the idef
(idef->ntypes * idef->ntypes entries).
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.
_______________________________________________
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
