AMBER Archive (2009)

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

From: Keith Van Nostrand (kifvan_at_yahoo.com)
Date: Wed Aug 19 2009 - 11:44:49 CDT

Peter,

  I have experienced similar difficulties using an improper dihedral coordinate across an RNA dimer structure.  The restraint did not image properly when the molecule was wrapped, and therefore changed the meaining of the restraint.  It was a difficult problem to spot.  I have thrown out a lot of data where this had occured.
  I have subsequently been able to reimage my simulation box and solute using the LOOS tool package ( http://membrane.urmc.rochester.edu/Software/LOOS/LOOS.html ), but nothing can correct simulations where the improper dihedral restraint became busted by irwap.

Sincerely,
Keith Van Nostrand

________________________________
From: Peter Varnai <p.varnai_at_sussex.ac.uk>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Wednesday, August 19, 2009 12:16:01 PM
Subject: Re: [AMBER] Distance restraint and periodic boundary conditions

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

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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