[gmx-users] umbrella sampling tutorial quastion

przemek bartha przemekbartha at gmail.com
Mon Jan 9 22:15:01 CET 2012

According to Justin's tutorial on umbrella sampling,
could anyone explain, if the molecules are restrained in any way in the
umbrella sampling part?
What I mean, is when we pull molecule A from molecule B, we restrain "B" to
that it does not follow "A" (by adding "pos_res" section in .itp file).
In my particular case, I pull asparagin asid (ASP) from lisyne (LYS), so I
have got two .itp files for both molecules. Restraining LYS worked well for
generating configurations, but failed for umbrella sampling.
My molecules (including LYS which was restrained) were "flying" randomly
all over the box which resulted in incorrect PMF courve.

So, during umbrella sampling, shall both the molecules be restrained, none,
or only one of them? Why?

thanks in advance,
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