[gmx-users] Basic Understanding about Gromacs C library

[Murilo Kramar]

Thanks for your answers and sorry for not describing my problem.


So, basically my problem is based on selections and some linear algebra
calculation. First of all I select a specific type of atoms and after that
I select a different group and calculate the angle of these atoms in
respect of a fixed point and other geometric properties.


If I'm correct I should use the '-selection' property by modifying this
struct (as in the second selection):


const char *mySel[] = {"name C"};


t_pargs pa[] = {

{"-cutoff", FALSE, etREAL, {&cutoff},

"Cutoff for distance calculation (0 = no cutoff)"},

{"-select", FALSE, etSTR, {mySel},

"Trying to do some selection"},

};


What I don't get is whether this selection is going to be passed to the
analyze_frame or not. Because if it does, then I need to do a further
selection that relies on the first one and I don't know how to proceed.


Thanks again,


Murilo.

On Fri, Jun 17, 2016 at 12:59 AM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> On 16/06/16 19:29, Murilo Kramar wrote:
>
>> Greetings, List,
>>
>> I have a set of data that I used to analyze through VMD. As the set is
>> quite heavy and there are many of them, using VMD was a bit cumbersome. So
>> it has been decided that working in GROMACS would present benefits.
>>
>> The first step that I executed was to compile via CentOs terminal  the
>> 'template.c' that comes with GROMACS 4.6.3 (the version that my group
>> works
>> with) in order to get used to its programming style. When it executes
>> there
>> is a 'header' telling some basic info about  the program (such as
>> command-line options used) and after that  I'm inquired to make selections
>> (to fill the -select option) . Where does this header come from? I'm
>> pretty
>> sure it is not coded directly in the 'template.c'. I ask this because I'm
>> trying to use the -select option inside the code, but it seems that I
>> can't
>> do that when I have this input asking.
>>
>
> You do not say what you are trying to analyze. Gromacs has many analysis
> tools ready to use.
>
>
>> I'm worried that this is a too simple question, but I'm really stuck at
>> this for 3 days. Pardon me if it is.
>>
>> Thanks in advance.
>>
>> Murilo G. K.
>> <gromacs.org_gmx-users at maillist.sys.kth.se>
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>
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