[gmx-users] fixing protein during energy minimization

Mark Abraham mark.abraham at anu.edu.au
Tue Feb 6 10:42:38 CET 2007

> Now if you think of following this last suggestion, don't bother.
> There's no point in doing EM on a frozen system :D

Well, that's a touch strong... you might want to do EM with a structure
frozen to optimize something else (here the extra waters), but that
doesn't make much sense in the context of MD system preparation, as you
point out below.

> Don't do EM in the
> first place then. The reason you want to do EM (and this is where the
> manual comes in handy) is to rid the crystal structure of bad
> contacts. So you DON'T want it NOT to change (you want it to change,
> that is). Besides, your crystal structure didn't include the hydrogens
> of your water molecule. So these will have to find a proper position
> anyway.


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