[gmx-users] Umbrella sampling of peptide-membrane system

[Mijiddorj B]

Dear John,

Thank you very much for your advice.

Best regards,
Mijiddorj

Hi,
>
> Justin's tutorial is not a fully generalized procedure for umbrella
> sampling; it shows a workflow for one specific example which is not always
> applicable to other systems.
>
> In general, you don't have to use position restraints for anything in
> umbrella sampling. Justin uses them to keep the fibril in place for
> specific reasons, as noted in the paper he based the tutorial on.
>
> That said, what are you trying to do? Adding restraints to the bilayer is
> probably a bad idea, seeing as how the motion of the bilayer is an
> important physical behavior.
>
> Are you calculating the PMF for a molecule traversing a lipid bilayer? If
> so, there are many examples in the literature that detail a procedure
> that's probably much more relevant to you.
>
> Best,
>
> John
>
>
>
> > Dear GMX users,
> >
> > I would like to ask about position restraint during the umbrella
> sampling.
> > 1. Is it need to make position restraint of lipid bilayer during the
> > umbrella sampling simulation?
> > 2. The position restraint was used for the B chain of amyloid-beta
> > peptides
> > in prof. Justin's tutorial. Can I run the simulations without position
> > restrain of lipid molecules in the case of lipid bilayer?
> > or
> > 3. Can I use the position restraint for only phosphorus atoms of the
> > headgroups of both leaflets?
> >
> > If you have any experience, please let me advise which one is better for
> > this kind of calculation.
> >
> > Best regards,
> >
> > Mijiddorj
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