Yes, try making all those steps longer, that should help.
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417
On Tue, Aug 24, 2010 at 4:48 AM, M. Reza Ganjalikhany
<ganjalikhany.gmail.com> wrote:
> 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
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 24 2010 - 07:00:03 PDT
