[gmx-users] xtc vs trr format
feenstra at chem.vu.nl
Tue Oct 28 09:01:13 CET 2003
Nuno R. L. Ferreira wrote:
> Hello gmx users
> By default mdrun saves .xtc files, so I assume that a great majority of you
> save the trajectories in this format.
> Is that right? And what about -ndec, do you use 3 or a greater precision?
> I think that we have to choose the precision accordingly to what we want to
> digg out from the trajectory.
> I'm performing some normal MD stuff, and it's time to save my information.
> My trajectories are in .trr format, and just wanted to ask for an opinion
> 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 100ps,
which I can use for quick analysis (e.g. an rmsd plot).
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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