[gmx-users] umbrella sampling tutorial quastion
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:
> According to Justin's tutorial on umbrella sampling,
> 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,
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