It is probably a good thread to share an odd experience using NMR
distance restraints between two molecules and octahedral periodic box
with iwrap=1. I used pmemd of amber9/10 and on occasional restarts of
the simulation from previous ascii rst file, the restraint distance
increased by about the size of the box and the corresponding restraint
energy was huge. These simulations then dragged the molecules across
the box quickly to satisfy the distance restraint. I noticed this
behaviour because the association of the two molecules was not the same
before and after these restarts. The EAMBER energy calculation considers
correctly the periodicity even if the molecules appear at a distance
apart due to wrapping on the fly. However it is not the same what iwrap
is doing with the coordinates when nmropt applies a distance restraint.
It is probably more complex that this as when a simulation starts from
molecules in proximity and then iwrap separates them virtually during
the simulation, it does not seem to affect the restraint energy in the
actual run, but after restart the behaviour described above will happen.
It became a bit tricky to run long simulations where I am forced to use
iwrap but the imaging puts the molecules in a different arrangement back
to the central box, eg. | A...B | can become | B...A|.
I wonder if people had similar experience.
Best regards,
Peter
case wrote:
> 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
>
--
Dr Peter Varnai
Department of Chemistry and Biochemistry
University of Sussex
Falmer, Brighton, BN1 9QJ, United Kingdom
T: +44 1273 873881, F: +44 1273 876687
E: p.varnai.sussex.ac.uk
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Received on Wed Aug 19 2009 - 23:33:23 PDT
