[gmx-users] Gromacs - MD run

Vytautas Rakeviius vytautas1987 at yahoo.com
Thu Apr 20 14:26:55 CEST 2017

Selected force field determines what will be pushed and what will be pulled during MD run. Which one you use? Maybe just try other.

    On Thursday, April 20, 2017 1:20 PM, Mariusz Wierzbowski <mariuszmw at gumed.edu.pl> wrote:

 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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