Dear Shafinaz
Please read the AMBER manual. There you'll find a description of how to
start an aMD calculation. Basically you have to run a regular MD
simulation to extract the average potential and dihedral energy. From
there you have to calculate the aMD parameters (look at the AMBER manual).
What you have to decide is if you want to run in explicit or implicit
solvent. With explicit solvent we recommend using a boost to both: the
potential and dihedral terms. If you use implicit solvent we recommend
accelerating only the torsion terms (dihedrals).
I hope this helps. If you have any further questions do write us back here
and we'll do our best to help you if you have any problems.
Best
Romelia
>
>
> Dear Dr. Roe
>
> Could you please advice how to perform acclerated MD available in Amber12.
>
> Do you have a input file and any instructions? I want to run Ace. MD on a
> protein about 250 residue long to observe some opening of a helix.
>
> Thanks in advance. I am waiting for your reply.
>
> Regrads.
>
> Shafinaz
>
>
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>
--
****************************************
Romelia Salomon
Walker Group
398 San Diego Supercomputing Center
UC San Diego
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Received on Mon Dec 03 2012 - 12:30:02 PST
