[gmx-users] Re: .mdp format

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 3 18:55:30 CEST 2008

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:


> 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.


> Thanks a lot
> Lin


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list