Re: Re: Cell Data in DCD files - CHARMM compatibility

From: Joshua D. Moore (
Date: Fri Aug 07 2009 - 22:26:07 CDT

Dear Dimitar,
You can check the VMD dcdplugin source file:

That will probably answer the questions about VMD.

I might be wrong, but I thought I had some experience testing flipdcd and
found that it didn't preserve the unit cell information (or wrote all 0s or
something....I can't remember exactly). fixdcd might be doing that. It
might help to look at the source ?

Are you by any chance running CHARMM on a different machine than you are
running NAMD? If the two machines are opposite endianness, this might be
the problem as well.

Another option might be to use catdcd. Since it uses the VMD plugins, it
understands the endianness of the file, so I often just use this from
machine to machine to convert the files. It also preserves the unit cell
information (at least I think it does).


On Fri, Aug 7, 2009 at 8:50 PM, Dimitar V Pachov <>wrote:

> I have prepared an Octahedral system in CHARMM (building, minimization,
> equilibration(in NPT)) and used the final coordinates as an input for
> testing runs in NAMD (2.6 and CVS version) that can after that be analyzed
> back with CHARMM. I defined CellBasisVectors in accordance with the CHARMM
> orientation of the OCTAhedral (i.e. the matrix of the vectors is symmetric).
> Then, I ran a short MD (100-200ps) and produced a DCD file with the
> "DCDUnitCell yes" option. The documentation claims this file is in CHARMM
> format and has to "contain unit cell information in the style of Charmm DCD
> files". However, when I read this NAMD produced trajectory file in CHARMM,
> it didn't seem to contain the correct "CHARMM style cell data". Why:
> 1) CHARMM + CORREL CELL module can extract cell data from trajectory files.
> I extracted the cell data (A,B,C, Alpha, Beta, Gamma + 6 lower diagonal
> values for the SHAPE symmetric matrix) from the CHARMM produced
> equilibration trajectory and compared it to the same data from the NAMD DCD
> file, and these data do not match. A,B,C values match (within fluctuation
> error), but while the CHARMM angles Alpha,Beta,Gamma are the correct 109.47*
> for OCTAhedral system, the NAMD trajectory gives values of 90.43* for all of
> the three angles. Also, the SHAPE matrices values are different.
> 2) Read the NAMD trajectory in CHARMM, build IMAGES within a certain cutoff
> based on the cell data for every frame in the DCD file, and save PDB files
> for the primary cell + the images. When looked in VMD, the images are very
> distorted and do not fill up the space around the primary cell (images
> attached).
> Therefore, my questions are:
> 1. Does NAMD actually save the unit cell data in the DCD file in a CHARMM
> compatible format? If it does, why am I having problems? If it doesn't, what
> is the format then?
> 2. I tried to use the FixDCD utility to change the header of the NAMD DCD
> file (assuming it was in a "wrong" X-Plor format) and reuse it in CHARMM for
> analysis, but the obtained new trajectory file was reported not to
> "...CONTAIN CRYSTAL UNIT CELL DATA". I compared its header to a CHARMM
> produced trajectory containing crystal data, and although the two header
> structures looked similar, it seemed that some data were missing from the
> fixed DCD file. Why is that?
> 3. Or, am I missing something?
> Thank you,
> Dimitar

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