read in multiple dcd from NAMD

[Nancy Deng]

I am new to the bio3D in R, but played with the tutorial. And I really like it.

I have multiple .dcd trajectory files from NAMD output, and they are every 250 ps interval.

So just wonder how to read in the multiple files.

I saw a post a while ago, but seems different format, just wonder whether anyone can help me out of this.

thanks a lot!!

Nancy

[Xinqiu Yao]

You can construct a loop to repeatedly read files and combine them afterwards. For example,

# suppose your DCD files are all ended with '.dcd.' and placed under the directory 'trajs' 
files <- list.file('trajs', pattern='.*\\.dcd$', full.names=TRUE)
xyz <- lapply(files, read.dcd)

# combine trajs into one matrix
xyz <- do.call(rbind, xyz)
class(xyz) <- c('xyz', 'matrix')

[Nancy Deng]

Thanks a lot xin-qiu for your promt response.

Just wonder whether I can call you for some brief discussion, such as how to interpret the PC analysis etc.

Best regards,

Nancy

Nancy Deng, Ph.D. | Principal Scientist, Computational Chemistry & Molecular Modeling Zoetis Inc| Global Therapeutics Research | 333 Portage Street, Kalamazoo, MI 49007 Office: 2693599121 | [e-mail]

[Xinqiu Yao]

Hi Nancy,

You are welcomed to ask questions! Create issues here or send Email directly to [e-mail].