[gmx-users] recalculating .trr from .xtc
x.periole at rug.nl
Tue Oct 15 09:16:57 CEST 2013
Interactions will be off, especially the bonded terms.
> On Oct 15, 2013, at 7:21, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> Also, the precision was selected when the xtc file was written, ie in the
> mdp file.
>> On Oct 15, 2013 3:24 AM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>>> 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
>> 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
>> 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 <jalemkul at outerbanks.umaryland.edu> |
>> (410) 706-7441
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