[gmx-users] umbrella sampling tutorial quastion

Dariush Mohammadyani d.mohammadyani at gmail.com
Mon Jan 9 22:36:40 CET 2012

As I know, it is not necessary to restrain neither reference nor pulled
group. When you apply pulling force, it means you have restrained both of


On Mon, Jan 9, 2012 at 4:15 PM, przemek bartha <przemekbartha at gmail.com>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?
> 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,
> Przemek
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Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15261
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