Thank you very much for your kind feedback !
In fact, I tried with the restrains = 1 and indeed it did not move
much meaning that the restrains significantly damped rmsf profile in
the restrained region... BTW dealing with a water-soluble protein
which has a small membrane-embedded domain, what force of the posters
should be applied on the membrane-bound part in order to freeze it in
the case of the simulation of the entire complex in water ??
Yours sincerely
Enrico
Il giorno ven 21 lug 2023 alle ore 13:35 David A Case
<david.case.rutgers.edu> ha scritto:
>
> On Fri, Jul 21, 2023, Enrico Martinez via AMBER wrote:
> >
> >btw what's about the force of the restraints? I've just noticed that
> >even with the restraint_wt=5.0 applied on the backbone, the structure
> >does not move. What's the difference between 1 and 100 and when do I
> >need the strongest restraints ?
>
> You should run some experiments yourself, with varying values of the
> restraint. That will tell you more than replies on the list. As an
> example, I don't know exactly what you mean when you say "the structure does
> not move": do you mean "does not move much" (which I would expect), or "does
> not move at all" (which would signal some sort of problem.)
>
> You don't need to answer the above questions -- running tests for yourself
> will help you gain confidence in what is going on.
>
> A value of 5 or 10 is a strong restraint; 100 is an extremely strong
> constraint, and could easily lead to problems with MD integration.
>
> ....dac
>
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Received on Fri Jul 21 2023 - 05:30:03 PDT
