Re: Kinetic Energy frm MDEnergy (energy evaluation tool)

From: Jan Saam (jan.saam_at_charite.de)
Date: Mon Mar 12 2007 - 19:13:31 CDT

Hi Rahul,

this is a bug in MDEnergy that I have fixed last week.
Please download the MDEnergy again and try if the new version works for you.

Regards,
Jan

---------------------------
Jan Saam
Institute of Biochemistry
Charite Berlin
Monbijoustr. 2
10117 Berlin
Germany

+49 30 450-528-446
saam_at_charite.de

> Hi all,
> I have tried to calculate the kinetic energy of the selected atoms by
> MDEnergy. In order to calculate this, I have mentioned the following in
> the command line:
> mdenergy -vel file-vel.dcd -dcd file1.dcd -psf file1.psf -par par-file1
> -beg 1 -end 400 -sel file2.ind -kin
> where,
> file-vel.dcd velocity dcd file
> file1.dcd structure dcd file
> file1.psf psf file
> par-file1 parameter file
> file2.ind selection file (which is the index file--the kinetic
> energy is to be calculated for this selection)
> This is the calculation for 400 frames.
>
> However, the output file is showing *zero kinetic energy for* each frame
> (kinetic = 0).
> Please explain me, why I am getting the value of kinetic energy as "0"
> for each frame ?
> I would highly appreciate any kind of help regarding this.
>
> Thanks
>
> Best Regards
> Rahul Bhowmik
> Grad Research Assistant,
> Department of Civil Engineering,
> North Dakota State University,
> Fargo, ND-58105.
> Phone :- 701-231-6275 (O)
> 701-231-4208 (R
>

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