Re: editing the code of the non bonded pair potentials

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Fri Aug 30 2013 - 18:00:08 CDT

Hi Victor!

Thanks for this link. I'm really curious about mindy. I have downloaded
it. Do you know whether it supports the CHARMM CMAP correction? It
probably also doesn't have the latest additions of NAMD like GBSA.
Nonetheless, an excellent starting point!

Gianluca

On Fri, 30 Aug 2013, Victor wrote:

> There's always Mindy. --Victor
> http://www.ks.uiuc.edu/Development/MDTools/mindy/license.cgi?files/mindy-1.0.src.tar.gz
>
>
> On 08/30/2013 02:47 PM, Kenno Vanommeslaeghe wrote:
>> 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)
>>>> {
>>>> 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
>> opinion.
>>
>> Cheers,
>>
>> Kenno.
>>
>>
>
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
                     http://healthynaturalbaby.org
-----------------------------------------------------

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