dcd file loading error

[Rahul Suresh]

R version 3.4.2 (2017-09-28) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.3 LTS

Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

My error:

dcd <- read.dcd("traj.dcd") NATOM = 65936 NFRAME= 5002 ISTART= 0 last = 5002 nstep = 5002 nfile = 5002 NSAVE = 1 NDEGF = 0 version 24 Reading (x100)Error: cannot allocate vector of size 7.4 Gb

How do I overcome it?

[Xinqiu Yao]

type ulimit -v in a linux shell and check if the number is too small (<7.4Gb). If so, enlarge it to e.g. 'unlimited', ulimit -v unlimited.

Caution: Make sure you have sufficient RAM to load the entire trajectory in R; otherwise, your system will become very slow. If RAM is limited, a better way is to reduce the number of frames to analyze by e.g. skipping every 5 frames or considering only last 1000 frames.