How to manage disk space for Gromacs XTC (trajectory) file output

User discussions
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1

I’m running and MD run with Gromacs.
Typically with this command:

gmx mdrun -v -deffnm md

It also produces trajectory file with .xtc extension.
Typically this file is extremely large, e.g. 143Gb for 1ns simulation and 143Tb for 10ns simulation.

My questions are:

  1. Is there an option in gmx mdrun to specify where to write the .xtc file?
    For example I want to specify specific directory path with large disk space.
  2. Is there away to shrink the size of .xtc file?
2

what is the interval freqency you saving the file? and what is the total size of the simulation system? 143 GB for 1ns seems huge.

See the output control in MDP setting

https://manual.gromacs.org/documentation/current/user-guide/mdp-options.html

3

I don’t think I’ve generated 143 TB of data in my entire career, let alone for a single 10-ns simulation. You’re probably saving far too frequently for a very large system, but without more details of what you’re doing, there’s nothing specific we can suggest to help.