Hi Reza,
On Wed, May 26, 2010 at 9:41 AM, M. Reza Ganjalikhany wrote:
> I have problem with adjusting the number of minimization steps for my MD simulation.
> I ran 3 MD simulations in explicit solvent with a protein containing 181 a.a. for 2 nanosec and I got
> 3 different sets of data in which the RMSd, RMSf, radius of gyration and
> other data were a bit different in each one!!
>
> Minimization steps were adjusted as below:
> run #1 : 2500 steps (1000steps steepest decent+1500 steps conjugate gradient)
> run #2: 5000 steps (2000 steps steepest decent+3000 steps conjugate gradient)
> run #3 :10000 steps (2000 steps steepest decent+8000 steps conjugate gradient)
You mention running 3 MD simulations, but the information you put here
is for minimizations. Can you clarify what you actually did?
> Is it normal to obtain different sets of data upon doing different minimization steps?
I'd say yes, it is normal. The potential energy surface for systems
this big is very complex, with many, many minima. A small change in
the minimizer parameters could easily take you to a different minimum,
and get trapped there.
> How many minimization steps should be sufficient? How is it possible to find
> ot its suficiency?
If you are trapped in different local minima, no number of steps will
help. Even if you could get all 3 results to the same structure, there
would be no guarantee that you are in the global minimum.
Is finding a global minimum really that important for your project? If
so, the best you can do is probably changing the minimizer to LMOD (se
manual). However, as Dr. Steinbrecher mentioned, the super-tight
minimization becomes just a waste of time if you intend to run MD with
it later. If the results you show in the pictures are from MDs run
**after** the minimizations you mention, then all it tells me is that
the runs are not converged yet. When converged, you should get the
same thermodynamic properties from any of the simulations.
Cheers,
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417
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Received on Wed May 26 2010 - 07:30:11 PDT
