Re: editing the code of the non bonded pair potentials

From: Kenno Vanommeslaeghe (
Date: Fri Aug 30 2013 - 13:47:15 CDT

On 08/30/2013 10:10 AM, Axel Kohlmeyer wrote:
> On Fri, Aug 30, 2013 at 12:26 PM, Asaf Farhi <> wrote:
>> If (E_VDW>E_c)
>> {
>> E_VDW=E_c;
>> f_VDW=0;
>> }
>> If (E_el>E_c)
>> {
>> E_el=E_c;
>> f_el=0;
>> }

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
> around.

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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