[gmx-users] Error in Umbrella sampling

Maziya Ibrahim maziya.ibrahim at gmail.com
Tue Jun 24 08:57:51 CEST 2014

Hello all,

I have been running the umbrella sampling tutorial available on the bevan
lab website.

After the following steps:

grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt
-o pull.tpr
mdrun -s pull.tpr

trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep

When I run the distances.pl file  I get this error:

"Fatal error:
Molecule in topology has atom numbers below and above natoms (451).
You are probably trying to use a trajectory which does not match the
first 451 atoms of the run input file.
You can make a matching run input file with tpbconv."

I do not understand what changes to make to rectify this error. Any
help is greatly appreciated.

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