On 21/11/2010 8:45 PM, Amit Choubey wrote:
Hi all,
I was going through the very nicely presented tutorial by Justin (on
KALP-15 in DPPC). I have one question regarding the non-bonded
cut-offs. It seems that people use many different values of non-bonded
cut-off (varying from 0.9 nm to 1.2 nm or probably more). How should i
choose the cut-off values for my simulations ?
In the first instance, by reproducing the conditions under which the
parameters were validated. Unfortunately, most of the force fields were
not parametrized for PME, under which they are often now used. So look
at some papers from large well-known groups that have done something
similar to what you want to do, judge how well they have worked, and do
something comparable. Unfortunately, there have been little or no
systematic studies of how accurate forcefield X plus PME needs to be to
model reality usefully. Hopefully that will change :-)
Mark
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