[gmx-users] Problem with MD simulation

Mariusz Wierzbowski mariuszmw at gumed.edu.pl
Wed Apr 19 12:45:10 CEST 2017

Hi, I am not sure if this is a problem. I performed md run for a protein(pdb 
code 1rep) and I am wondering when i convert file from last ns with gmx 
editconf -f md25.gro -o md25.pdb and look at the pdb, the ds DNA seems 
divied, splitted there is one half with the protein and the second one 
bellow. Is this normal or is it wrong ? Where could I have made a mistake, 
the RMSD chart for this protein after simulations looks good.

Thanks for all suggestions.


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