[gmx-users] Re: xtc vs trr format

Nuno R. L. Ferreira nunolf at ci.uc.pt
Tue Oct 28 17:15:01 CET 2003


Tkx for the tips Anton.


> Nuno R. L. Ferreira wrote:
> > Hello gmx users
> >
> > By default mdrun saves .xtc files, so I assume that a great majority of
> > save the trajectories in this format.
> > Is that right? And what about -ndec, do you use 3 or a greater
> > I think that we have to choose the precision accordingly to what we want
> > digg out from the trajectory.
> >
> > I'm performing some normal MD stuff, and it's time to save my
> > My trajectories are in .trr format,  and just wanted to ask for an
> > about a "safe" format to put in the CD (several, by the way).
> > After that, the analyses could be made in any other precision.
> I use the default ndec=3, that is sufficient for all types of analysis
> that I ever heard of. I tune nstxout/nstvout so that a frame is written
> to .trr file every few hours along the calculation (usualy every 10-50ps).
> Depending on how much disk is on the machine I run on, I either write the
> whole system to .xtc every 1 ps, or I only write protein(s) + substrate(s)
> co-factor(s). That, I also put on CD (or, recently, on DVD!). Then, I make
> one .xtc file with only the 'protein+stuff' in it (if I haven't got that
> already), and a few ones with less frames, like every 10 ps and every
> which I can use for quick analysis (e.g. an rmsd plot).

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