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.
http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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