From: Andrew Jewett (
Date: Fri Aug 08 2008 - 14:15:46 CDT

>>On Jul 24, 2008, at 3:17 AM, pellegrini wrote:
>> Is there a way or an option (I did not find it in the manual) to
>> get a single dcd file of
>> 1ns using the the first 500ps of my simulation that was interrupted
>> and the 500 other ps
>> coming from a restart ?

>From: Eric H. Lee (
>Date: Thu Jul 24 2008 - 08:58:21 CDT
>Yes, you can use the tool catdcd to join dcd files.

  This is a helpful answer, but it doesn't quite resolve our issues.
I have a feature request for both catdcd and NAMD. (I hesitate to
cross-post this question to the NAMD mailing list, but perhaps I

  In our lab, we run thousands of short simulations, one after
another. (There are several reasons we are forced to do this.) We
don't know in advance how many there will be. After each one, we
append the most recent trajectory to the end of the existing
trajectory. We are using catdcd to take a pair of input trajectories
and merge them into a new output trajectory. As the trajectory gets
longer, the time required to do this gets longer, because each time,
catdcd must create a new file and we delete the old trajectory. As
the file gets larger, we end up spending more time waiting for catdcd
than we do waiting for the simulation to run.

  I know there are smarter ways to use catdcd. (Catdcd can merge
more than two files together. We could wait until the end, and use
catdcd to merge all of the files together, but it's not a very pretty
script. We don't know how many of them there will be, but there are
typically more than 10000. Considering that we have multiple
replicas, we have hundreds of thousands of them. This has brought
down our file-system before.)

  How hard would it be to modify catdcd so that it appends trajectory
data to existing files (instead of creating a new file)? If this is a
feature that already exists in catdcd, please change the documentation
to clarify this. (Assuming catdcd is written in C or C++, I'd be
happy to try adding this feature. I was thinking of using "-a
outputfile" instead of "-o outputfile". Is that okay? Not sure if
I'm up for to digging into the NAMD source code, yet.)