[gmx-users] recalculating .trr from .xtc

Justin Lemkul jalemkul at vt.edu
Tue Oct 15 03:23:19 CEST 2013

On 10/14/13 7:56 PM, Leandro Bortot wrote:
> Dear GROMACS users,
>       Does anyone know how significant is the difference between the
> "original" .trr file from a simulation and a "recalculated" .trr from a
> whole system .xtc (mdrun -rerun traj.xtc -o traj.trr)?
>       I mean... do you know how big would be the error induced by this
> "recalculation" procedure?
>       I'm not interested in calculating autocorrelation functions. Most of
> my analysis are related to the atom positions over time and free energy
> calculations.

Position-related quantities should be impacted very little.  Given that you 
can't acquire precision though, I see no point in even generating a .trr file - 
the .xtc has the same information while occupying less disk space.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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