[gmx-users] interaction lists in idef.h

[wnoid at hec.utah.edu]

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 <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] interaction lists in idef.h
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <46DCFD17.2000404 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> wnoid at hec.utah.edu 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.
>>
>>