[gmx-users] number of coordinates in coordinate file does not match topology

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 19 03:06:05 CET 2012

Acoot Brett wrote:
> Dear All,
> I am practicing the on-line tutorial 
> http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/.
> In the step "mdrun -v -deffnm 1LW9-EM-solvated" of "Energy minimization 
> of the solvated system", it says "
> Converged to machine precision  , but not to the requested precision 
> Fmax < 1". Before this step, all the other steps run fine.
> In the step "grompp -v -f pr.mdp -c 1LW9-EM-solvated.gro -p 1LW9.top -o 
> 1LW9-PR.tpr" of "Relaxation of solvent and hydrogen atom positions: 
> Position restrained MD", it says "
> Fatal error:  number of coordinates in coordinate file 
> (1LW9-EM-solvated.gro, 32748) does not match topology (1LW9.top, 0)"
> I am looking forward to getting a reply from you on how to what leads to 
> the error message.


You need to make sure the contents of the [molecules] directive always matches 
that of the coordinate file, in terms of the number of molecules and the order 
in which they are present.



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


More information about the gromacs.org_gmx-users mailing list