Yes, as we read the long time scaled MD paper from Deshaw group, they
prefer CHARMM27 FF. If we read the methods and materials,which probably
most people forget to care about, we always find the following sentence:
/All simulations used the CHARMM27 force field for protein, ions, and
water (51, 52); the//
//CHARMM36 force field was used for lipids (53). Torsional backbone
corrections: U = k·Σm//
//(−1)m−1 · [(1 + cos m(φ − φ'))/m!], (m = 6 and k = 9.2 kcal·mol−1),
centered at φ' = φxtal − 180°;//
//were applied to SF residues Gly376 and Gly378 to prevent SF
degradation on a timescale of//
//microseconds (21); φxtal ~ 50° and φxtal ~ 100° for these residues in
the crystal structure (10)./
here is full text for it, in page 2 you can find those statements.
That's why I asked if nowadays Amber FF good enough for such kind of
purposes.
best
Albert
On 11/21/2012 01:37 PM, David A Case wrote:
> On Wed, Nov 21, 2012, Albert wrote:
>> >
>> > I've got a question for the Amber99-ILDN and recent Amber12SB FF. Are
>> >they good enough for long time scaled MD simulation such as tens of
>> >microsecond ?
> The answer must depend on the type of system (protein?) you are planinng
> to simulate, and how you define "good enough". The DEShaw group has
> reported long simulations with the ILDN modifications to Amber99SB, and
> the modifications involved in ff12SB are of a similar nature. My group
> has done a number of 1-2 microsecond simulations of very stable proteins
> that show good structural equilibration and no long-term drift, using
> ff12SB. But the generic question you proposed is surely unanswerable.
>
> ....dac
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Received on Wed Nov 21 2012 - 06:00:04 PST
