AMBER Archive (2009)

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

From: Peter Varnai (
Date: Wed Aug 19 2009 - 11:16:01 CDT

I would like to add the following:
there was an extensive discussion about a similar topic on the reflector
"pmemd iwrap trouble" started on Aug 25 2008. There Tom Cheatham
suggested a possible tweak of the prmtop file purposes that might be
useful when simulating two separate solute molecules. I wonder if that
tweak could prevent iwrap separating the complex thereby causing trouble
when distance restraint is used. I tested sander (amber10) that behaves
identically to pmemd; this really is an issue to deal with when
molecules are separated due only to imaging but nmropt takes the
coordinates "as is" after restart; all seem fine if separation happens
during the simulation.


Peter Varnai wrote:
> 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

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