[gmx-users] abnormal RMSD

[Justin A. Lemkul]

>
> " 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.

-Justin

>
> with regards
>  Anamika
>



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Justin A. Lemkul
Graduate Research Assistant
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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