Dear Prof. Case
I'd be grateful if you could expand / clarify the last statement
Of course, none of these reservations apply to those using Amber(tm) force
fields....]
It is not clear, at least to me, what you mean
Regards
George
Sent from my iPad
On 18.10.2012, at 03:09, David A Case <case.biomaps.rutgers.edu> wrote:
> On Wed, Oct 17, 2012, vaibhav dixit wrote:
>
>> Checking rmsd is an essential part of the MD trajectory analysis and it
>> helps us to validate if the system has reached equilibrium (converged) i.e.
>> expected to be closer to what would a real protein/DNA/any other system
>> would be.
>
> I think you need to be careful here. "Convergence" of a simulation
> means that it has relaxed into a structural basin that represents what the
> force field thinks the protein ought to be doing. This might be a long way
> from what the "real" protein does. If the starting structure is derived from
> good experimental data, conformations seen after equilibration may well be
> further away from the "real" result than the starting structure. And the
> longer you run, the worse things may get.
>
> [Of course, none of these reservations apply to those using Amber(tm) force
> fields....]
>
> ....dac
>
>
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Received on Wed Oct 17 2012 - 18:30:03 PDT
