Thank you for your help,
Actually I perform the equilibration as long as heating.
Finally, 15ns MD simulations have been done at NPT.
On Mon, Aug 23, 2010 at 6:28 PM, Gustavo Seabra <gustavo.seabra.gmail.com>wrote:
> I agree with Bhavaraju:
>
> It is unlikely that the difference in the RMSF comes from use if
> iwrap. As I mentioned in my first reply, your heating is indeed too
> fast, so it is very likely that none of your calculations is
> converged.
>
> First, 20 or even 40ps is too small a time for heating. Myself, I
> usually do that in at least 2 steps: 100ps to take the system from
> 0-100K, then another 100-150ps to take the system from 100 to 300K
> (NVT). Of course, that can vary depending on the system.
>
> Then comes the constant pressure part. You don't mention how long that
> equilibration was, but it should be long, probably longer than the NVT
> simulations. For some systems, for example, I have used up to 2ns, but
> that again can depend on the system.
>
> Finally, you also don't mention what are the conditions of the final
> 15ns simulations. Is it NPT, NVT, NVE, etc?
>
> Cheers,
> Gustavo Seabra.
>
> On Mon, Aug 23, 2010 at 5:03 PM, M. Reza Ganjalikhany
> <ganjalikhany.gmail.com> wrote:
> > Thank you for your email.
> >
> > I'm looking for local fluctuations in a psychrophilic enzyme at different
> > temperatures (278,308 and 333). I found a meaningful difference at the
> first
> > experiment which was not reproduced on the iteration.
> >
> >
> >
> > #1: (iwrap=0)
> >
> > A- Heating system with weak restraints on protein in 20 ps with constant
> > volume from 0 K to (278,308 and 333) K
> >
> > B- Equilibration at constant pressure at (278,308 and 333) K
> >
> > C- Three sets of 15 ns MD simulation at (278,308 and 333)K
> >
> >
> >
> > #2: (iwrap=1)
> >
> > A- Heating system with weak restraints on protein in 40ps (constant
> volume)
> > from 0 K to (278,308 and 333) K
> >
> > B- Equilibration at constant pressure at (278,308 and 333) K
> >
> > C- Three sets of 15 ns MD simulation at (278,308 and 333)K
> >
> >
> > Finally I found RMSFs from experiment #1 completely different with #2 at
> > certain positions. On the other words, the fluctuation at certain
> positions
> > has been decreased with the temperature in #1 which was reversed in #2.
> >
> > The differences in these experiments are including the heating time and
> the
> > imaging (iwrap).
> >
> >
> >
> > RMSFs are attached.
> >
> >
> >
> > Regards,
> >
> > M.Reza
> >
> >
> >
> > On Mon, Aug 23, 2010 at 7:26 AM, Gustavo Seabra <
> gustavo.seabra.gmail.com>wrote:
> >
> >> Although it is true that you may be using a equilibration time that is
> >> too small, and that your heating is too fast, especially since you are
> >> using explicit solvent, the main difficulty in answering your question
> >> is that you also don't mention what properties you are looking at. How
> >> did you conclude that your results after 15ns are "completely
> >> different"? What properties did you measure? How do they differ?
> >>
> >> Note that, even with the exactly the same protocol, the precise
> >> trajectories and final structures are expected to differ between two
> >> different simulations.
> >>
> >> Cheers,
> >> Gustavo Seabra
> >> Professor Adjunto
> >> Departamento de Química Fundamental
> >> Universidade Federal de Pernambuco
> >> Fone: +55-81-2126-7417
> >>
> >>
> >>
> >> On Mon, Aug 23, 2010 at 6:01 AM, M. Reza Ganjalikhany
> >> <ganjalikhany.gmail.com> wrote:
> >> > Dear all,
> >> >
> >> > I have done two similar MD simulations with a 300 a.a. protein in
> >> explicit
> >> > solvent with different equilibration time.
> >> > The first equilibration time was 20ps and the second was 40 ps (from 0
> K
> >> to
> >> > 300 K) and then I got completely two different results after 15ns MD
> >> > simulations.
> >> >
> >> > Is it normal to obtain such results? How long should be sufficient for
> >> such
> >> > system to be equilibrated?
> >> >
> >> > Any help would be greatly appreciated.
> >> >
> >> > Regards,
> >> > M. Reza
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Received on Tue Aug 24 2010 - 01:00:03 PDT
