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

From: Ashkan Shekaari (
Date: Wed Jul 14 2021 - 06:30:22 CDT

Dear researcher,
As I mentioned before, ligand is very small, then:

    * timestep becomes very important, you presumably have to use timesteps less than 1
    * taking into account quantum mechanical considerations becomes very important depending on the problem
    * periodic interactions become very important, use boxes with > 20 Angstrom padding, or use spherical BCs for being more safe.

I have also seen people having exactly the same issue using GROMACS; therefore, it has nothing to do with the computational code you are working with.

Ashkan Shekaari
PhD Candidate in Solid State Physics
Department of Physics
K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ ] [;!!DZ3fjg!uTJZNZx1FuisMA2jYpHB7jK77HOf3qCyEKrIRXnBocvFN3I072JPsBm7qb8Y4pPMmg$ ]

From: "Nancy Singh" <>
To: "namd-l" <>
Sent: Wednesday, July 14, 2021 3:46:58 PM
Subject: namd-l: Protein-ligand complex is coming out of the water box

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


This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:11 CST