From: Asaf Farhi (asaf.farhi_at_weizmann.ac.il)
Date: Fri Aug 30 2013 - 13:55:21 CDT
Thank you very much!
I'll look for switching function.
Will be happy to hear the future recommendations.
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Kenno Vanommeslaeghe [kvanomme_at_rx.umaryland.edu]
Sent: Friday, August 30, 2013 9:47 PM
Subject: Re: namd-l: editing the code of the non bonded pair potentials
On 08/30/2013 10:10 AM, Axel Kohlmeyer wrote:
> On Fri, Aug 30, 2013 at 12:26 PM, Asaf Farhi <asaf.farhi_at_weizmann.ac.il> wrote:
>> If (E_VDW>E_c)
>> If (E_el>E_c)
Asaf, it looks like you're introducing a discontinuity in the first
derivative. While this is OK for MC, it violates the underlying
assumptions that make the Verlet integrators used in MD well-behaved.
You'll be needing a switching function.
> (...) then you probably should modify an MD
> code that is simpler to understand and modify. there are many of those
Axel, sorry for going a bit on a tangent here, but purely out of
educational interest, can you give a pointer to one (or more) from the top
of your head? A quick Google search turned up toyMD, but since you appear
to be more knowledgeable in these things than I am, I'd like to know your
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