[gmx-users] Why my protein always falls out of the water box?

Jochen Hub jhub at gwdg.de
Mon Mar 13 15:45:12 CET 2006

Shanjie Huang wrote:

>Hi dear friends,
>I performed a molecular dynamics of a ligand-receptor complex for 5ns;
>but I found that my complex always fall out from the water box quickly
>in the first 1ns. What may be the problem? 
>Can I constrain some residues which are far away from the active site to
>aviod this problem? But I am worry about the extra constrain would
>interfere my MD result, for in the normal situation there should be no
When using

comm-grps                = Protein

in your mdp file the center of mass of you protein will stay at its 
starting position.

good luck,

Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de

More information about the gromacs.org_gmx-users mailing list