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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