[gmx-users] How to draw a RMSD plot after essential dynamics analysis(EDA)

Erik Lindahl lindahl at csb.stanford.edu
Mon May 10 10:37:31 CEST 2004

> but when i hit the enter, it display a fatal error: Molecule in 
> topology has atom numbers below and above natoms (597).You are 
> probably trying to use a trajectory which does not match the first 597 
> atoms of the run input file.You can make a matching run input file 
> with tpbconv.
> I do not know what happened about it. please give me a detailed 
> interpretation because i am a new user og gromacs. I doubt that there 
> are fault command line or parametters used above. If they are 
> incorrect, please give me a correct ones. My aim is to calculate a 
> RMSD for the first 8 eigenvectors as a function of alpha carbons. 
> so,you may also tell me the procedure on how to draw such RMSD plot 
> useing gromacs modules.

The problem is likely that you filtered the trajectory to only contain 
CA atoms, but your .tpr file still containts all atoms, so obviously it 
doesn't match.  Use the program tpbconv to create a custom tpr file 
with only CA atoms.



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