Hello,<br>According to Justin's tutorial on umbrella sampling, <br>link: <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html</a><br>
could anyone explain, if the molecules are restrained in any way in the umbrella sampling part?<br>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).<br>
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.<br>My molecules (including LYS which was restrained) were "flying" randomly all over the box which resulted in incorrect PMF courve.<br>
<br>So, during umbrella sampling, shall both the molecules be restrained, none, or only one of them? Why?<br><br>thanks in advance,<br>Przemek<br>