[gmx-users] Basic Understanding about Gromacs C library

[Christopher Neale]

Writing your own analysis tool in template.c might not be the best solution either. You have to worry about things like pbc breaking and you in many cases need to write routines that already exist elsewhere. I suggest looking into standalone analysis kits such as http://loos.sourceforge.net/ or http://www.mdanalysis.org/ (I am sure there are others too). While you can write your own core analyses in these tools using python or in some cases C, the libraries to do the transformations you want are generally available already.

As to your exact question, I presume the header is written by the function CopyRight() .. you're asking about the part of the output that starts ":-)  G  R  O  M  A  C  S  (-:", right?

I'm not sure how to stop the program for asking for input, I but I presume you could set it inside the program and then pipe some nonsense in at runtime to make the selections and it should work for now until somebody else responds as long as you set the value after the input is read (and exit statement spamming throughout your program can helpyou to figure out what function is responsible).

Chris.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Murilo Kramar <mkramar at u.rochester.edu>
Sent: 16 June 2016 13:29:16
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Basic Understanding about Gromacs C library

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.

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>
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