Hi!!
You can run aMD with any AMBER executable (sander, pmemd or pmemd.cuda).
You just need to include in your input file the lines specifying the aMD
parameters you want to use
iamd type of aMD calculation
EthreshD threshold energy for the dihedral energy
alphaD strength of dihedral boost
EthreshP threshold energy for the total potential energy
alphaP strength of total potential boost
and that is it! Well, you need to run a short regular (no aMD) MD to
determine the value for the parameters mentioned above, but that is all
(check the manual).
> Hi,
>
> I wish to run a aMD simulation with amber. How can I go about doing it?
>
> With regards,
> Yew Mun
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
****************************************
Romelia Salomon
Walker Group
398 San Diego Supercomputing Center
UC San Diego
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Received on Mon Jul 08 2013 - 17:00:02 PDT
