Re: Protein-ligand complex is coming out of the water box

From: René Hafner TUK (
Date: Wed Jul 14 2021 - 06:27:23 CDT

Hi Nancy,

     its not unexpected that it might move and might cross borders, but
with wrapAll on the atoms should be wrapped back (resulting in long bonds).

     Check the logfile if all those parameters got parsed correctly.

     You can wrap the trajectory around the protein using the very fast
implementation qwrap;!!DZ3fjg!rMKLQ9m3-wylw4U29SWTjXOuaeNcLtUghl30P_YydcBTvP44NBMJuV0HgFHXvepQDQ$ .



On 7/14/2021 1:16 PM, Nancy Singh wrote:
> Hii,
> I have done the protein-ligand simulations with namd for 10ns. But the
> problem is after 5ns protein and ligand complex starts to move out of
> the box. I have already put  wrapALL, wrapNearest and wrapWater as ON
> but still the complex is coming out of the box. Is there something
> wrong with simulations or it is natural for protein to move from one
> periodic cell to another?
> and How can I tackle this if I want to make th animation of my trajectory?
> Thank You
> Regards,
> Nancy

Dipl.-Phys. René Hafner
TU Kaiserslautern

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