Re: Re: recalculating energy using dcd file

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Wed Aug 05 2009 - 09:58:22 CDT

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.

Josh

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?
>
> Thanks
>
> Rabab
>
>
>
> ----------------------------------------------------------------------------------------------------------
>
> NAMDenergy should be able to give you what you need:
> http://www.ks.uiuc.edu/Research/vmd/plugins/namdenergy/
> On May 7, 2008, at 9:19 AM, gurvisha_at_leadinvent.com 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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