Re: namd energy self interaction reality check

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Nov 25 2008 - 08:00:25 CST

Hi Thomas,
please note that with PME off and switcing on, changing the cutoff has a
profound effect on the electrostatic potential (see
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node24.html for why). With a
cutoff at 30 A you may want to turn switching off, which will give exact
electrostatics and have a negligible effect on the vdw energies.
Best,
Peter

Thomas C. Bishop wrote:
> Greetings namd,
> I'm using namd to calculate energies from an existing trajectory w/ the
> tcl scripting capabilities.
>
> I am only calculating "self interaction energy" for a group of atoms
> that's w/in a bubble of radius 30A.
>
> I expect that once the cutoff is large enough to include all atoms in
> my group (30A bubble) that the electrostatic and vdw energies won't
> change as a function of cutoff...
>
> But this is not happening. the vdw and elec energy changes up to a
> cutoff of over 100A... bond,angle,dihed remain constant as function
> cutoff for any given snapshot (as expected)
>
> here's relevant section of my namd.conf file.
> I've run the calcs w/ cutoff from 8A up to 100A and elec and vdw
> continues to change... but the atoms in my system are all w/in 30A of
> each other..I thought after 30A nothing would change.
>
> what am I missing? (i've checked that the group is really the group I
> think it is)
>
> it's late hopefully someone will provide an answer by morning...
> final note PME is off so it's not a size scaling effect.
>
> thanks for any insight/input.
>
> Tom
>
>
>
>
> margin 2.0
> switching on
> switchdist 8.0
> cutoff 10.0
> pairlistdist 12.0
>
> pairInteraction on
> pairInteractionCol B
> pairInteractionSelf on
> pairInteractionGroup1 1
> pairInteractionFile select.pdb
>
>
>
>
>
>
>

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