Re: Calculating interaction energy in NAMD

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Sun Mar 28 2010 - 13:50:38 CDT

Hi,

You can use *coorfile* to read your dcd trajectory and turn on
*pairinteraction* to calculate energies between atoms.
Some example can be found here: http://bessie.che.uc.edu/wiki/NAMD_post-processing

Best,
Bin

On Mar 28, 2010, at 2:28 AM, DimitryASuplatov wrote:

> Hello,
>
> I am using namd2.7b1in AMBER mode. I have the input amber topology and
> parameter files, output dcd trajectory and log files written with one
> timestep.
> How do I calculate energy between two atoms I select for each time
> frame during my trajectory?
>
> Thank you.
> SDA
>

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