[gmx-users] abnormal RMSD

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 15 18:31:42 CET 2008

> " Molecule in topology has atom numbers below and above natoms. you are
> probably trying to use a trajectory which does not match the first 330 atoms
> of the run input file. You can make a matching run input file with tpbconv."

Use the same .tpr file that you submitted to mdrun to generate the trajectory. 
It has the reference structure for your simulation (t=0).  Try with -pbc nojump
and -pbc whole to see which reconstructs your system appropriately.


> with regards
>  Anamika


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


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