[gmx-users] Large output files and limited disk space. How do I handle them?

Mark Abraham mark.abraham at anu.edu.au
Mon Aug 9 07:55:50 CEST 2010

----- Original Message -----
From: NG HUI WEN <HuiWen.Ng at nottingham.edu.my>
Date: Monday, August 9, 2010 13:17
Subject: [gmx-users] Large output files and limited disk space. How do I	handle them?
To: gmx-users at gromacs.org


> Dear gmxusers, >   > I have a very basic question here which I hope someone could help me with. I was running a couple of simulations over the weekend on a shared cluster and both came to a stop for the same reasons:  >   > Program mdrun_mpi, VERSION 4.0.7
> Source code file: trnio.c, line: 252 > File input/output error:
> Cannot write trajectory frame; maybe you are out of quota? >   > Indeed there were quite a number of large files in my user directory (e.g. the .trr files and etc). I think the problems probably arise from the fact that (i) I am storing my trajectory as full precision .trr files and (ii) setting too small a value for nstxout and nstvout in .mdp.  >   > I have seen some tutorials that suggested using "trjconv" to derive the reduced precision .xtc files from the .trr files and then discard the latter. My question is, would this be wise as I am not sure whether I would find myself needing these .trr files in the future. >   > Here's a snippet of my .mdp file. Am I saving my coordinates and velocities too frequently? If I were to increase this, are there any compelling factors that I need to take into considerations?
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 500000        ; 2 * 500000 = 1000 ps (1 ns)
> dt              = 0.002         ; 2 fs
> ; Output control
> nstxout         = 100           ; save coordinates every 0.2 ps
> nstvout         = 100           ; save velocities every 0.2 ps
> nstenergy       = 100           ; save energies every 0.2 ps
> nstlog          = 100           ; update log file every 0.2 ps

See  http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume

Unless you know you need full precision data for some expected  analyses, I'd expect most people want nstxout/nstvout every few  nanoseconds to enable restarts (possible, but unlikely to be needed).  For most analyses, using nstxtcout with suitable output groups is at  least an order of magnitude more space-efficient. Also consider how  large nstenergy should be.

Mark |

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