AMBER Archive (2009)

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

From: Peter Varnai (p.varnai_at_sussex.ac.uk)
Date: Thu Aug 20 2009 - 10:23:48 CDT

Dear Dave,

Thanks for your response. It is hard to avoid the need to use nmropt
with iwrap when one does umbrella sampling in explicit water for 100ns<.
I think binary restart files (ntxo=0) are no longer allowed (amber10).
It would be good to re-enact this option though. Until then I wonder if
some tweak could force iwrap to consider the complexed molecules as one:
pmemd has a variable "no_intermolecular_bonds" which could redefine the
complex as one fused molecule if I introduced some covalent linkage
(with zero force constant) between the subunits. To correct my restart
files with separated subunits (to continue simulation) I will use ptraj
and image the subunits back to a complex, write out this restart file
and then paste the velocities from the old restart file... would be nice
if ptraj could also dump the velocities from the restart file after
imaging.

best regards,
Peter

case wrote:
> On Wed, Aug 19, 2009, 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.
>>
>
> Thanks for the detailed report. The bottom line from my perspective is:
> don't use iwrap=1 if you can possibly avoid it. In particular, don't use
> iwrap=1 with NMR-like restraints in place.
>
>
>> 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.
>>
>
> I think iwrap only affects output coordinates, not the internal ones the
> program is using. This would explain the behavior you report.
>
>
>> 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|.
>>
>
> For Amber developers: it seems to me that the "correct" solution here is
> to allow binary restarts, so that no one is "forced to use iwrap". Plus, we
> could have wrapping code in just one place (ptraj), where there is logic to
> have greater control over how wrapping is done that we have in sander/pmemd.
>
> So, is there something broken with binary restarts in the current
> code? [The unformatted form doesn't have ltemp0; I don't know what else
> might or might not be broken.] If someone could look into this (Scott?)
> it would be a great help. This is important enough that we should consider a
> patch to Amber10, if needed.
>
> ...thanks...dac
>

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