[gmx-users] Storage of large output files

Monika Sharma mon_sharma at research.iiit.ac.in
Thu Aug 9 11:48:52 CEST 2007

Thanks Mark for your reply. Thats a sound advice. I will really take 
care of. Actually, through my previous mail, I wanted to know that what 
other groups are using as storage devices for the backup of their large 
files, that must have figured out that which way is best-" economical 
and efficient" way to store their data.

Mark Abraham wrote:
> Monika Sharma wrote:
>> Dear All,
>> We have started our venture into MD recently, for which we are using 
>> our in-house resources. Now that MD runs are giving very large output 
>> files like for trr files. The files keep piling up and using spaces 
>> on the work machines. This is creating problems with the depletion of 
>> space with every run. Can anyone please suggest an "economical and 
>> efficient" way how to take backup of such a large files of the order 
>> of Gb or so, so that we dont end up piling up our work machines with 
>> such files. And the data need to be saved for future references..
> First, consider whether you are producing more output than you need. 
> Look at the options for output frequency of positions and velocities 
> in .trr files, whether you should be using .xtc files, and whether you 
> should only be outputting subsets of your data.
> Normally you only want a full frame of positions and velocities in 
> your .trr file with frequency with which you might ever want to do an 
> exact restart (and make sure your energy output frequency is a 
> suitable multiple so you also have energies at this time). This 
> frequency is invariably much smaller than the frequency with which you 
> want output data. If you only want position data for your solute for 
> your later analysis, then outputting only that group to an .xtc file 
> with frequency as low as you'd ever need will be a tiny fraction of 
> the cost of a .trr file of the whole system with positions and 
> velocities at every step. Be aware that analysis types that require 
> autocorrelation functions need data sampled much more frequently than 
> the characteristic times of the system.
> Mark
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