[gmx-users] Break ? => Position restrained MD

[Mark Abraham]

Chih-Ying Lin wrote:
>  
>  
> Hi
> In the position restrain MD, only solvent molecules and hydrogen atoms 
> are allowed to move...

.... appreciably under normal conditions. However if you have a medium 
restraining force and a ridiculously large LJ force, guess who wins?

> I checked the .out file.
> The max is happened on the atoms inside protein.
> Why?

Probably because they were overlapping with some other atoms initially.

Try setting up a simpler simulation system until you work out how to get 
things right. Definitely record each step as you do it (e.g. copy and 
paste your terminal history after using "history") so you know what 
you're doing where.

Mark