Hi,
> I want to unfold my protein by heating it up to 400K, then following by MD
> run to expect it re-fold again. I got some results (png attached), but Im
> not sure that it was unfolded with that temperature.
> I viewed the results using VMD, but I got confused with the differences of
> using *rst* and *crd* files.
> The *rst* showed me the "full" structure while the *crd *showed me the
> "scattered" structure, especially in the MD frames.
The pictures from the crd files look more like representation errors, you
do not say how you loaded the structures in vmd, but if the final crd
snapshot and the final rst look considerably different, something is wrong
(and it might not be Amber). VMD has several options about input formats
and if you specify the wrong one, it still tries very hard to load the
coordinates anyway, often leading to strange looks.
You dont specify how long you simulated, but from the rst files, I would
say your protein is definitely not unfolded. My guess would be that even
if you manage to completely unfold your protein, there is no good reason
to expect it to quickly refold during another simulation, but your
literature sources may tell you otherwise for this special case...
I wouldnt define folded and unfolded by just looking at the structure,
instead rmsd-values, number of Hbonds, trajectory clustering or radius of
gyration measurements over the trajectory should give you a lot more solid
information...
> Btw, I found a related issue in AMBER forum, and Jason said that "*The
> restart is actually a full time step ahead with the coordinates (and a
> **half
> time step ahead for velocities)", may I have it more clearer?
Check e.g. Allen, Tildesley, "Computer simulations of liquids", 1987
Clarendon Press, or any other textbook that explains the different types
of verlet propagators. This is not related to your unfolding question,
though.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Mon Sep 19 2011 - 01:00:04 PDT
