[gmx-users] gmx_ana_selcolletion_t definition

[MURILO GABARDO KRAMAR]

Greetings,

Using version 5.1.2 of Gromacs I was able to develop the selection system
in the proper maner. Thanks again.

Now I have a new doubt about it. I ran both the VMD script that I had
developed previously and the Gromacs code and their results differ. After
futher investigation I've noticed that the selections handed different
results.

I guess that this two statements should be equivalent:

VMD: "(within 9 of index 11776) and (name C) and (not index 11776) "
Gromacs: ""(within 0.9 of atomnr 11776) and (name C) and (not atomnr 11776)"

But running it on VMD I detect 39 atoms and when I run it on Gromacs I
identify only 1 atom.

The same occasion happens whenever I use the following selection strings:

VMD: "(within 6 of index 11776) and name OW"
Gromacs: "(within 0.6 of atomnr 11776) and name OW"

This time VMD finds 1 and Gromacs finds 31.

Is there anything that I didn't detect that make them different?

Thanks.

2016-07-14 9:25 GMT-06:00 MURILO GABARDO KRAMAR <
murilokramar at alunos.utfpr.edu.br>:

> Hello again,
>
> I've talked to my adviser and we agreed to install version 5.1. I'll take
> a look in the documentation and try to work on it.
>
> Murilo.
>
> 2016-07-13 10:19 GMT-06:00 MURILO GABARDO KRAMAR <
> murilokramar at alunos.utfpr.edu.br>:
>
>> Hello Mark,
>>
>> Thanks for you answer,
>>
>> My concern about using a newer version is that there are other people in
>> the group where I'm working at that use this exact version. =(
>>
>> Do you think that using this version I can accomplish the selections
>> task?
>>
>> Murilo.
>>
>>
>>
>>
>>
>>
>> 2016-07-12 15:21 GMT-06:00 Mark Abraham <mark.j.abraham at gmail.com>:
>>
>>> Hi,
>>>
>>> 4.5.3 is really old version of GROMACS. You might have a better time
>>> with a
>>> more recent version, perhaps with better docs. Or maybe you don't need to
>>> write code at all if you ask people first. :-)
>>>
>>> Mark
>>>
>>> On Tue, Jul 12, 2016 at 9:56 PM MURILO GABARDO KRAMAR <
>>> murilokramar at alunos.utfpr.edu.br> wrote:
>>>
>>> > Hello,
>>> >
>>> > I've managed to solve the inclusion problem by adding it to the .pc
>>> files
>>> > inside pkgconfig folder.
>>> >
>>> > Now I'm trying to implement the above mentioned, but I can't really do
>>> > that. I'm trying to update the 'selstr' field inside
>>> > 'gmx_ana_selcollection_t *sc' and then calling
>>> > 'gmx_ana_selcollection_evaluate()', but this doesn't seem to be the
>>> correct
>>> > path to make new selections inside 'analyze_frame()' since the
>>> following
>>> > code does not update the selection:
>>> >
>>> >         //Selects all the waters near the guest molecule
>>> >         sprintf(d->sc->sel[WATER]->name, "(within 6.0 of %i) and name
>>> OW",
>>> > d->sc->sel[GUEST]->p.m.mapid[i]);
>>> >         d->sc->sel[WATER]->selstr =  d->sc->sel[WATER]->name;
>>> >         rc = gmx_ana_selcollection_evaluate(d->sc, fr, pbc);
>>> >
>>> > Here 'i' is a simple for-loop index variable. GUEST maps to the value
>>> zero
>>> > and WATER to value one.
>>> >
>>> > Murilo.
>>> >
>>> > 2016-07-08 10:59 GMT-06:00 MURILO GABARDO KRAMAR <
>>> > murilokramar at alunos.utfpr.edu.br>:
>>> >
>>> > > Hello List,
>>> > >
>>> > > I'm developing a analysis program based on tamplate.c of Gromacs
>>> 4.5.3.
>>> > In
>>> > > order to do so, I intend to use the function
>>> > > gmx_ana_selcollection_evaluate() along with modification of the name
>>> > field
>>> > > within the structure gmx_ana_selection_t inside analyze_frame
>>> function().
>>> > >
>>> > > The gmx_ana_selcollection_evaluate() requires the usage of
>>> > > gmx_ana_selcolletion_t which I put inside the following structure:
>>> > > typedef struct
>>> > > {
>>> > > gmx_ana_selection_t *refsel;
>>> > > FILE *fp;
>>> > > FILE *fp2;
>>> > > real *ave;
>>> > > real *n;
>>> > > gmx_ana_nbsearch_t *nb;
>>> > >
>>> > > //
>>> > > gmx_ana_selcolletion_t *sc;
>>> > > } t_analysisdata;
>>> > >
>>> > > Whenever I compile my program it doesn't recognize
>>> gmx_ana_selcolletion_t
>>> > > which resides in 'selcolletion.h', but I don't know where to find
>>> this
>>> > file
>>> > > in Gromacs include folder so I can proper include it.
>>> > >
>>> > > Thank you all,
>>> > >
>>> > > Murilo.
>>> > >
>>> > --
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>>
>>
>