Error in loading dcd file: shows much higher NATOMS than the actual: can not allocate memory

[pullak pullak]

Dear sir, i am a new bio3d user. I wanted to do the trajectory analysis of my system. my pdb and dcd files are going fine with vmd and also not big (1949 atoms,1000 frames, a total of 25mb ). when i load the dcd file, the error says:can not allocate memory of vector size 75 Gb It shows the NATOM=67108871, which was not expected.

Also i have checked ulimit -v and it is unlimited. I find people are using much bigger dcd files for their calculations. please see the sessioninfo as given bellow.

dcd2 <- read.dcd("1st_1000frames.dcd")

NATOM = 67108871 NFRAME= 1000 ISTART= 0 last = 1000 nstep = 1000 nfile = 1000 NSAVE = 1 NDEGF = 0 version 24 Error: cannot allocate vector of size 750.0 Gb

> sessionInfo()

R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.5 LTS

Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale: [1] LC_CTYPE=en_IN.UTF-8 LC_NUMERIC=C LC_TIME=en_IN.UTF-8 LC_COLLATE=en_IN.UTF-8
[5] LC_MONETARY=en_IN.UTF-8 LC_MESSAGES=en_IN.UTF-8 LC_PAPER=en_IN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] igraph_1.2.2 bio3d_2.3-4

loaded via a namespace (and not attached): [1] compiler_3.4.4 magrittr_1.5 parallel_3.4.4 tools_3.4.4 Rcpp_0.12.18 grid_3.4.4 pkgconfig_2.0.2

-pullak

[pullak pullak]

Anyone Please have a look into this. I am stuck here.

[pullak pullak]

hello sir/madam,

I am eagerly waiting for your comments

[Xinqiu Yao]

Hi,

Can you provide an small example DCD file that we can reproduce the problem?

[pullak pullak]

Hi,

I have loaded the dcd file along with its psf file in vmd and then retrieved the same by saving the dcd coordinates via vmd toolbars, and now this is working with bio3d. i am not sure what has exactly happened by retrieving the same data again, but the good thing is: it is working now in bio3d.
I doubt whether i have installed all the dependencies for bio3d, because now i am stuck with another stuff. This is as follows:

view.cna(net_cutoff0.5, pdb)

**Error in view.cna(net_cutoff0.5, pdb) :

could not find function "view.cna"**

your valuable comments will be highly appreciated.

[Xinqiu Yao]

Hi,

The function name has been changed to vmd.cna().

[Xinqiu Yao]

Original problem resolved. Additional problem is due to name change of the function.