Re: how does namd handle violations of the minimum image convention?

From: Boyang Wang (pkuwangboyang_at_gmail.com)
Date: Tue Jan 10 2012 - 21:45:04 CST

Hi Ana,

as a non-expert, I remember that NAMD manual explained how PME calculates
the summation over infinite number of periodic boxes. It should be
characteristic.

There should be experts that write codes where topology could be targeted.

Boyang

On Mon, Jan 9, 2012 at 7:32 PM, Ana Celia Vila Verde <acavilaverde_at_gmail.com
> wrote:

> Hi everyone,
>
> I recently ran (by mistake) a simulation where the cutoff distance was
> slightly larger than L/2. I was expecting to get blatantly unphysical
> results for violating the minimum image convention, but it turns out that
> my protein behaves just fine: results are very similar to simulations of
> the same system in which the minimum image convention is not violated.
>
> Out of curiosity (I don't have any inclination to go about performing any
> more simulations like this), can someone explain how namd handles
> violations of the minimum image convention, for both PME and VDW?
>
> I searched the namd-list and found one message indicating that using
> rcutoff>L/2 is (numerically) OK for PME because, since with PME we're
> calculating full electrostatics anyway, rcutoff simply changes the distance
> beyond which electrostatics are calculated using PME. As for VDW, I'm
> guessing what happens is that the rcutoff actually becomes L/2 instead of
> being larger than L/2. Can someone confirm this?
>
> Thanks,
>
> Ana
>
>

-- 
Boyang Wang, Ph.D.

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