[gmx-users] Error in MD simulation

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 25 18:48:57 CEST 2012

On 4/25/12 12:45 PM, vinee2here wrote:
> Hi all!!
> I am running a MD simulation of a protein modelled by using modeller...and I
> am getting an error in the grompp command.
> The error reported was : Number of coordinates in coordinate file
> (z_b4em.gro) does not match that of topology file (z.top). We are however
> not able to run the nohup command because of the above mentioned error.
> The link for em.mdp and the output obtained is :
> http://s1064.photobucket.com/albums/u378/vinee2here/
> Your help in resolving this issue would be highly appreciated.

The fatal error should have also printed a URL that you can follow to find this 


The solution to that particular error is always the same - keep track of your 
molecules better.  Use of the -p flag with genbox and genion to allow the 
programs to do the bookkeeping for you eliminates the majority of the problems.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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