Re: FW: ABF error calculation

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Fri Dec 11 2009 - 12:03:34 CST

Dear Valeria:

There are two options here that might be suited for your purpose:
1 : Namd *pairInteraction* option, which will output vdW and
electrostatics forces for a group of atoms.
2 : the Tcl command *loadtotalforces* available in tcl force script,
which will provide you all the force filled by that atom.
These can all be done in postprocessing.

You might also want to take a look at this link here : http://bessie.che.uc.edu/w/index.php?title=NAMD_post-processing&redirect=no

Hope this helps,
Best,
Bin

On Dec 11, 2009, at 9:04 AM, Valeria M. wrote:

>
> Dear NAMD Users :
>
> I want to compute the error in ABF calculations, as it is explained
> by Rodriguez et. al. I understand that I need the instantaneous
> component of the force, but I don't know how can I get it. I mean,
> I've already done the energy calculation, and I want to get the
> instantaneous force, but I don't want to run the ABF calculation
> again. Is it possible to get this information with a short run?
>
> Thanks in advance,
>
> Valeria.
>
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