Re: Re: recalculating energy using dcd file

From: Mert Gür (gurmert_at_gmail.com)
Date: Thu Aug 06 2009 - 15:09:58 CDT

Hi Rabab,
You can use NAMDenergy as a script.In other words you can just call it on
the tclconsole. In that case there is no need to load the dcdfile into VMD.
I think if you do it that way you will have no memory problems. Maybe you
are already doing it that way. In that case I am sorry to restate what u
already did :)
Best,
Mert

On Wed, Aug 5, 2009 at 5:43 PM, Rabab Toubar <rtoubar_at_yahoo.com> 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<gurvisha_at_leadinvent.com?Subject=Re:%20%20recalculating%20energy%20using%20dcd%20file>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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