[gmx-users] recalculating .trr from .xtc

[XAvier Periole]

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.
> 
> 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>
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 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