On Tue, Aug 18, 2009, Cyril Falvo wrote:
>
> I am trying to use Amber 9 to perform a restrainted MD simulation with
> periodic boundary conditions. I want to restraint the length of hydrogen
> bonds in an "infinite" beta-sheet and I am using the option /nmropt=1./
Just to add to Tom Cheatham's comment: Amber cannot handle an "infinte" sheet
using periodic conditions: you cannot have any bonds, angles or torsions that
cross the periodic boundaries. I can understand a desire to do this, but it
would require major changes to the code (i.e. to more than just the NMR
restraint stuff...)
...dac
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Received on Wed Aug 19 2009 - 23:30:03 PDT
