Maybe you should visit the manual for your last questions.
In my paper I have also followed the Justin’s tutorial however I did not use
restraint because for my purpose it was unnecessary.
Justin used it because restraining one peptide makes the remaining four
peptides more stable.
> On 13 Jan 2017, at 11:47, Emil Marklund <emil.markl...@icm.uu.se> wrote:
> I am trying to calculate PMFs for a number of protein-protein complexes,
> doing pulling and Umbrella sampling mainly following the protocol found in
> Justins tutorial.
> In my case it feels like I should remove position restraints in the umbrella
> sampling on the peptide that is kept stationary with pos. restr. in the
> pulling. And that also seems to be the consensus when reading older messages
> in this mailing list, that positon restraints should not be used in the
> umbrella sampling if you have no special reason to keep them (that the
> umbrella potential is enough to maintain COM separation). I am however a
> little confused since I can also find examples in the litterature where
> restraints seems to have been kept during umbrella sampling for reasons that
> is not always clear to me...
> Should I in this case remove positons restraints in the umbrella sampling?
> What does setting pull_coord1_type = umbrella actually do, is the COM
> distance between the proteins restrained or is the COM of each protein
> restrained to a position in space? If it is the first scenario can't you end
> up with problems if the proteins start to rotate around there joint center of
> mass and thereby aproaches the edge of the box?
> Emil Marklund
> PhD Student in Molecular Biotechnology
> Elf lab
> Department of Cell and Molecular Biology
> Uppsala University
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