Re: [AMBER] Re-Imaging Trajectories

From: Jason Swails <>
Date: Tue, 9 Jul 2013 23:06:07 -0400

Well I had a response typed out, but it was not as instructive as Dan's.
 Since I did have one footnote that he didn't, I'll add just that below.

On Tue, Jul 9, 2013 at 10:47 PM, Daniel Roe <> wrote:

> [snip]
> > In terms of NVE simulations would it be advantageous to run a
> > short 1-2 ns simulation, re-image the trajectory, and then use the new
> > trajectory coordinates to continue with a full 20 ns NVE simulation?
> As far as I know re-imaging the trajectory should have no affect on
> the dynamics. The one exception is possibly if you have distance
> restraints, which I think are not imaged.

GPUs complicates things a little. Because it uses single precision in some
locations and enables us to run insanely long simulations, there are times
when the values of the coordinates become so large as to swamp out too many
significant bits. When you calculate the image that belongs in the
'simulated' cell, you are effectively subtracting two huge numbers, leaving
you with a very uncertain value for the particle positions (a recipe for
  In this case, the particles need to be re-imaged back into the central
cell before they move too far to become a problem. However,
if you just use "iwrap=1"
in the mdin file
(and use the 'unwrap' function cpptraj when you need to study diffusion
properties), you should never have a problem.

A groupmate of mine recently ran a ca. 640 ns simulation without wrapping
on the GPUs, and about halfway through the simulation devolved into NaNs
and ****s for this very reason. Adding iwrap=1 (and nothing else) fixed
his problems.

Good luck,

P.S. It seems I am an amateur nitpicker today. In principle, Dan's right
in that imaging has no effect on dynamics, but the very real limitations of
single precision as it's used in Amber in certain places warrants a
mention, IMO (especially since 500 ns simulations are now routine).

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Tue Jul 09 2013 - 20:30:02 PDT
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