[gmx-users] umbrella sampling tutorial quastion
Justin A. Lemkul
jalemkul at vt.edu
Mon Jan 9 22:32:52 CET 2012
przemek bartha wrote:
> According to Justin's tutorial on umbrella sampling,
> could anyone explain, if the molecules are restrained in any way in the
> umbrella sampling part?
The umbrella potential itself is a restraint.
> 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).
The position restraint used during steered MD in the tutorial is different from
the umbrella restraint, practically and conceptually. Please refer to the
associated paper for the underlying reason. Position restraints are not
necessarily required for any umbrella sampling process.
> 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.
This sounds like more of a problem related to system construction rather than
anything related to restraints, i.e. you have one molecule at the edge of a
> So, during umbrella sampling, shall both the molecules be restrained,
> none, or only one of them? Why?
In principle, no restraint aside from the umbrella potential itself is required
to carry out umbrella sampling.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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