[gmx-developers] Re: Howto customize the output from the source

[David van der Spoel]

Jian Zou wrote:
> Dr. David van der Spoel,
> 
> Sorry for the inconvenience and thank you so much for your reply.
> 
> I saw in bondfree.c that some parts around the "if(debug)", there are
> "ifdef DEBUG" preprocessing statements (for example, in function
> "bonds"). Do I need to add a similar statement around my code and
> recompile with some special flags?
If the output is in between #ifdef you probably need to write all the 
way up the in bondfree.c file

#define DEBUG

> 
> The -debug option is for mdrun only and not for grompp, am I right? I
> cannot find this option using -h.

Debug is in most programs. Try the -h -hidden flags.

> 
> 
> Regards,
> 
> Jian
> 
> On Mon, Oct 6, 2008 at 10:17 AM, David van der Spoel
> <spoel at xray.bmc.uu.se> wrote:
>> Jian Zou wrote:
>>
>> Please put further questions on the developer list.
>> You can use the following:
>>
>> if (debug)
>>  fprintf(debug,"Value is %d\n",value);
>>
>> if you recompile and run with -debug you will get a file mdrun.log with your
>> output.
>>
>> Note that you can use tabulated bonded functions from gromacs 4 onwards.
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
>> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
>>
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-developers-request at gromacs.org.


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++