Dear all,
I have one more question for the equilibration routine for water
soluble protein.
Would the protocol consisting of 10 short steps: gradually decreasing
the force constant from 50 to 1 (with the step of 5) be valid or
rather it would be better to do it from 10 to 1 with the step of 1 ?
Personally I did it always in the first way (from 50) and I never have
seen any problems in the production run but probably would it be
better to try with more soft restraints ?
Cheers,
Enrico
Il giorno ven 21 lug 2023 alle ore 14:08 Enrico Martinez
<jmsstarlight.gmail.com> ha scritto:
>
> 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
> >
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 21 2023 - 07:00:02 PDT
