AMBER Archive (2009)

Subject: Re: [AMBER] Distance restraint and periodic boundary conditions

From: case (case_at_biomaps.rutgers.edu)
Date: Tue Aug 18 2009 - 21:02:45 CDT

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

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber