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

[NG HUI WEN]

Hi guys

 

Thanks for your help! I will consider your suggestions.

 

Huiwen

 

From: NG HUI WEN 
Sent: Monday, August 09, 2010 11:05 AM
To: gmx-users at gromacs.org
Subject: Large output files and limited disk space. How do I handle
them?

 

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

 

Many thanks for your help!

 

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