[gmx-users] recalculating .trr from .xtc

[Mark Abraham]

Also, the precision was selected when the xtc file was written, ie in the
mdp file.

Mark
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
>> 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
>
> --
> ==============================**====================
>
> 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
>
> ==============================**====================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>