[gmx-users] Re: .mdp format

[Chih-Ying Lin]

Hi
I think that
 include           =-I/my_working_directory
is redundant

and that is the fatal error coming from......


without this command (delete from my .mdp file)
 include           =-I/my_working_directory


my simulation get run

Thanks
Lin


On 7/3/08, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
>  Chih-Ying Lin wrote:
>
> > Hi
> > if I am in my working directory,
> > and give the command in my .mdp file
> >
> > include           =-I/my_working_directory
> >
> >
> > I will get the following error....
> > Program grompp, VERSION 3.3.3
> > Source code file: grompp.c, line: 469
> > Fatal error:
> > number of coordinates in coordinate file (xxx.gro, 24)
> >             does not match topology (xxx.top, 0)
> >
> >
> >
> >
>
>  When you get error messages, the first step should be to do a thorough
> search of the wiki (wiki.gromacs.org) and the mailing list archive.  If you
> had done this, you would have come across:
>
> http://wiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>
>
> > With Justin explaination,
> > More or less, yes.  By default, Gromacs searches $GMXLIB and the current
> > working directory for the necessary topology information.  The "include
> > = -I" line can be used to specify the location(s) of other necessary
> > topologies.
> >
> > Does it mean that I could simply delete the
> > "include=-I/my_working_directory" command??
> >
> >
> >
>
>  Yes, including the working directory would be redundant.
>
>  -Justin
>
>
> > Thanks a lot
> >
> > Lin
> >
> >
> >
>
>  --
>  ========================================
>
>  Justin A. Lemkul
>  Graduate Research Assistant
>  Department of Biochemistry
>  Virginia Tech
>  Blacksburg, VA
>  jalemkul[at]vt.edu | (540) 231-9080
>  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>  ========================================
>
>