From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Tue Sep 04 2007 - 20:13:35 CDT
Dear NAMD list users,
I have been trying to carry out unfolding simulations of Ubqiuitin. I use
the top_all22_prot.inp and par_all22_prot.inp topology and parameter files.
I did the following steps:
a) Energy minimization
b) Heating to 300K
c) Equilibration for 50ps NPT
d) Production run @300K for 1ns. NPT
e) Heating to 500K
f) Equilibration for 50ps NPT
g Production run @500K for 12ns NPT
Very surprisingly, I don't see the RMSD values changing (with respect to the
final equilibrated frame at 300K) by greater than 4-5 Angstroms. This is
very weird. There is a paper in Physical Review E, 72, 051928, 2005
"Unfolding dynamics of the protein ubiquitin: Insight from simulation" where
they achieved drastic unfolding within 1ns
for ubiquitin at 520K. I followed what they did and tried at 520K too.
I have used NPT throughout.. but I also used NVT and NVE ensembles.. and in
all cases it seems to be very stable. Does anyone have any pointers to what
I might be doing wrong?
Thanks in Advance,
Arun
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