Dear M. Reza,
> I think it is true in the case of data similarity.
> However my results seem to be similar, but I guess my RMSF sets are
> different significantly in some residues in each simulation.
> Is it still normal to have such variation is some residues?
> > > 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!!
You ran explicit solvent simulations for just 2ns so yes it is normal to
have such variation because you are probably way short of being converged.
Note this is not related to the minimization you did, all you did there was
generate 3 slightly different starting structures that then rapidly
diverged. This is similar to if you had used different random seeds for each
one.
A good test would be to try calculating your radius of gyration based on the
first 1ns, the second 1ns and the period 0.5ns to 1.5ns and then compare the
results. If you see variation similar to your other simulations then this is
a good indication that your results are not converged.
Good luck,
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
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Received on Wed May 26 2010 - 09:00:03 PDT
