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

[John Whittaker]

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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