Re: [AMBER] wrap warning

From: Jason Swails <>
Date: Thu, 29 Jan 2015 08:45:26 -0500

On Thu, 2015-01-29 at 14:54 +0200, Fabian Glaser wrote:
> Thanks!
> Related to this, is it necessary anymore to align trajectories made in
> separated ns runs before to restart a new ns run?

No. It has never been necessary. Aligning a restart file *might* cause
a slight change in the initial energy due to precision issues, but
certainly aligning a trajectory will never have an effect (it's not used
as input to the next simulation, after all).
> I noticed in the past that if I don't realign between ns, the initial
> energies and rmsd analysis of EACH ns production has a starting jump
> (slight destabilization) in values when trajin and analyzed. Is this
> solved by using ioutfm=1
> and ntxo=2 ??

How slight? It's possible this is a precision issue (i.e., ASCII
restarts do not store the full precision of coordinates), which would be
"solved" using NetCDF restarts.

However, note that the restart file is a time step *ahead* of the final
energy written to the mdout file, so the final energy of one simulation
will be one time step behind the first energy of the next. This could
also be the cause of your energy "jump".


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jan 29 2015 - 06:00:02 PST
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