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

[Jochen Hub]

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
>constrains. 
>
>Thanks.
>
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

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