simon sham wrote:
Hi,
I have recently done two simulations on a protein at high temperature
near its melting temperature. At the beginning I used CHARMM forcefield,
and then OPLSAA to double check the results. There are some differences
in the structures between the forcefield used. I know different
forcefields can give different results. All parameters in the
simulations were the same except the forcefield. Is there anyway I can
tell which forcefield gives more reliable results?
Compare with experimental results. Without something to compare to, each is
just a prediction of some unknown phenomenon. Keep in mind that a single
trajectory for either is not necessarily conclusive of anything. Replicates and
good sampling will be more informative.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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