On Tue, May 24, 2005, Simon Whitehead wrote:
>
> Previously i have been using the ff94 in the simulations of my protein
> (using amber4) and now i have upgraded to amber8 i am unsure which
> forcefield is most appropriate. At present i am using ff03 but dont know
> whether it would be more appropriate to use ff02(EP) which if i am right
> carries off point charges? Further to this, the protein i am runing dynamics
> on is quite large (110KDa) and due to its structure means that a large
> number of waters are required to solvate it in a periodic box so that
> sufficient room is left between the protein and the boundaries of the box.
> Please could you tell me if the solvent shell would be just as appropriate
> to use and is it not possible to run constant volume ensembles?
>
First, be sure that your really need to simulate such a large system,
especially if you are unfamiliar with force fields and the differences between
them.
We have had some reasonable results with ff02EP, but mostly on systems about
an order of magnitude smaller than you are discussing. Note that ff02 and
ff02EP are polarizable force fields, and hence significantly slower than more
conventional examples. The Adv. Protein Chem. review listed at the top of the
Amber web page could be a good start for you; ff03 is certainly a very usable
force field.
....hope this helps...dac
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Received on Wed May 25 2005 - 06:53:00 PDT
