Re: NAMD Energy types

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Sep 08 2010 - 19:19:02 CDT

Hi Lada,
Could you send the config file generated by namdenergy (namd-temp.namd)
and the top 10 lines or so of your pdb?
Thanks,
Peter

On 09/08/2010 05:16 AM, Lada Biedermannová wrote:
> Hi all,
>
> I am using the NAMD Energy plugin to get internal energies of a
> selection of my system. However, I am confused by the fact that I am
> getting a non-zero Bond, Angle and Dihed energies even for a selection
> of two atoms that are not bonded, eg. for two CB atoms as shown below.
> Could somebody explain where these numbers come from?
>
> Thanks,
>
> Lada Biedermannova
>
> ------------------------
> namdEnergy) Computing energy for selection:
> namdEnergy) index 6 16
>
> namdEnergy) Running:
> namdEnergy) /sw/mcm/app/namd/NAMD_2.6_Linux-i686/namd2 namd-temp.namd
>
> Frame Time Bond Angle Dihed
> Impr Elec VdW Conf Nonbond
> Total
> 0 0 +0.1559 +0.0737 +1.1857
> +0 -0.9343 -0.0181 +1.4153 -0.9524
> +0.4629
>

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