Re: dcd file format

From: Hyonseok Hwang (danggi_at_northwestern.edu)
Date: Fri Nov 24 2006 - 20:47:42 CST

Hi, Leandro

 From NAMD 2.6, the default value of 'DCDUnitCell' option is 'Yes',
which means that the information of the cell size (=simulation box) is
automatically written in each frame if you use periodic boundary
condition. Until 2.5, 'No' was default value. The cell size information
includes the x, y, z length of the simulation box and three angles. If I
remember correctly, each variable has double size and there are dummy
integers in front and behind the cell size information. So total size is
4 + 6 * 8 + 4 = 56 Bytes. The 56 Bytes are taken in front of the
coordinations in each frame. So you have to consider this if you want to
read a DCD file from 2.6. If you want more detailed information on DCD
file structure, please see the "dcdlib.C" among the NAMD source codes.
I hope this will be of help.

Best,

-Hyon

Leandro Martínez wrote:
>
> Hi all,
>
> I had fortran programs to read the dcd file format generated by version
> 2.5 of namd.
> Now it seems that in version 2.6 there has been a chenge in the DCD
> format and
> the programs do not seem to be able to read the coordinate files anymore.
>
> Previously I read the dcd files using:
>
> open(10,file=dcdfile,status='old',form='unformatted')
> read(10) dummyc, nset, (dummyi,i=1,8), dummyr, (dummyi,i=1,9)
> read(10) dummyi, dummyr
> read(10) ntotat
> do i = 1, nframes
> read(10) (x(i,j),j=1,ntotat)
>
>
>

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