But besides AMBER12, do other versions of AMBER accept the aMD input file?
On Tue, Jul 9, 2013 at 7:55 AM, Romelia Salomon <romelia.caltech.edu> wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards
Yip Yew Mun
Graduate, Masters
Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
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Received on Tue Jul 09 2013 - 01:30:03 PDT
