[gmx-users] Problem with MD simulation

[Marlon Sidore]

Hi,

you forgot about periodic boundary conditions - you need to put your
trajectory through trjconv -pbc mol to make your protein whole again.

On Apr 19, 2017 12:45 PM, "Mariusz Wierzbowski" <mariuszmw at gumed.edu.pl>
wrote:

> 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.
>
> Mariusz
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