Re: Re: recalculating energy using dcd file

From: Rabab Toubar (
Date: Thu Aug 06 2009 - 09:06:21 CDT

Thanks Josh,

While searching the mailing list for the problem I found about the Bigdcd, but I didn't find more info about it in the UG or the tutorials.
Has anyone tried the Bigdcd and can let me know how to use it


Rabab Toubar

--- On Wed, 8/5/09, Joshua Adelman <> wrote:

From: Joshua Adelman <>
Subject: Re: namd-l: Re: recalculating energy using dcd file
To: "Rabab Toubar" <>
Cc: "namd-l" <>
Date: Wednesday, August 5, 2009, 10:58 AM

Hi Rabab,
You could use catdcd to break the dcd into smaller parts and then analyze them one at a time, and then join the log files back together. I guess the other option is to use bigdcd, although I have never played around with this. The later may be preferable if you don't want to double the memory used on your hard drive by duplicating the trajectory in smaller pieces.

On Aug 5, 2009, at 7:43 AM, Rabab Toubar wrote:
 Hi all,
I want to extract energies from the dcd file to create a log file. Searching the mailing list, I got a similar post with a reply from JC Gumbart to use NAMDenergy (Post quoted below). Now I get to the problem of the dcd size as it is bigger than what the computer memory can handle, and I donot really want to "stride" it, as I want to consider all the frames.

Is there a way to egt around this problem?ThanksRabab

NAMDenergy should be able to give you what you need:
 On May 7, 2008, at 9:19 AM, wrote:
> Dear namd users
> I have a DCD file from a prior dynamics run but have lost its log file. I
> want to calculate the energy of each frame. Is there a way i can
> regenerate the log file using dcd file?
> Regards
> Gurvisha Sandhu


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