[gmx-users] Gromacs - MD run

[Mark Abraham]

Hi,

Your strands and protein are different molecules. Trjconv can't know you
intend them to function as a single unit unless you describe one. Probably
with the -cluster option.

Mark

On Thu, 20 Apr 2017 12:20 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
>
> Mariusz
>
> P.S
>
> 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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