On 28/05/2011 2:05 AM, Peter C. Lai wrote:
On 2011-05-27 10:50:14AM -0500, 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?
Also you never stated what RMSD/RMSFs between the two and if they are
significant to what you care to see (i.e. if you expect, say, alpha
helix to random coil transition, what changes in the unfolding do you see
that make you suspect one forcefield is better than the other?). Also if this
is in a solvated system, the rest of the forcefield has been parameterized
with the implicit assumption that TIPS3P (Charmm-specific) water will be used
so make sure you have switched your water type when using CHARMM.
Not necessarily required. See http://dx.doi.org/10.1021/ct700053u and
http://dx.doi.org/10.1021/ct900549r
Mark
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