Dear All,
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?
Many thanks
Simon Whitehead
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue May 24 2005 - 09:53:00 PDT
