[gmx-users] umbrella sampling tutorial quastion

Justin A. Lemkul jalemkul at vt.edu
Mon Jan 9 22:32:52 CET 2012

przemek bartha wrote:
> Hello,
> According to Justin's tutorial on umbrella sampling,
> link: 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html
> 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 
periodic boundary.

> 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
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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