[gmx-users] Gromacs - MD run

Mariusz Wierzbowski mariuszmw at gumed.edu.pl
Thu Apr 20 12:19:43 CEST 2017

Dear Gromacs users,

I am not sure what is the problem with my init file, I have a pdb file 
1rep.pdb i performed mdrun for it for 150 ns. After each run(I divied the run 
to 5 ns steps, it gave me 25 runs)I perfomed all of the runs. Than I wanted 
to check if the pdb files were ok. I checeked the pdb file gained from gro 
file with ediconf and the pdb looked good, the model looked stable for 16 
steps. Then I checked the nr 17 step and the model has ds DNA splitted into 2 
ss DNA one is close to the protein and second is below the protein. This 
situation is for rest of the steps from 17-25. What could go wrong? What is 
the possible explanation of this? Any suggestions ?

Thanks for all the help



Earlier I got a suggestion that I should perform -pbc nojump but that does 
not affect the gro file so the pdb still looks bad.

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