Dear friends,
Here is a quick update:
so finally I changed my equilibration protocol decreasing gradually
strength of the restrains from 10 (during the heating) to 0.1 (in
final phase) through 10 steps (10,9,8,7 ... 1, 0.1) and then performed
a 10 ns MD keeping only very weak restrains (0.1) to a small part of
the protein, which normally should be embedded in the membrane. The
visualization of this benchmark shows that everything looks realistic
but I did not notice a big difference in the stability of the complex
compared to my initial protocol using higher restraints (from 50 to 1)
. I would be grateful for any further suggestions, which could help
me to further calibrate the protocol.
Yours sincerely
Enrico
Il giorno ven 21 lug 2023 alle ore 15:37 Enrico Martinez
<jmsstarlight.gmail.com> ha scritto:
>
> 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
> > >
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Received on Mon Jul 24 2023 - 08:30:02 PDT
