Re: 1-5 Intramolecular repulsions

From: Rebecca Lindsey (linds360_at_umn.edu)
Date: Wed Nov 05 2014 - 13:07:49 CST

Kenno,

Re-reading, I can see how that was unclear. The TraPPE force field uses an
additional 1-5 repulsion term between O and H atoms to prevent excessive
intramolecular hydrogen bonding. This term, when summed together with the
LJ term, gives the vDW term.

Jeff,

That is indeed the case.

Thanks for your replies.

On Wed, Nov 5, 2014 at 12:51 PM, Jeffrey Potoff <jpotoffx_at_gmail.com> wrote:

> Hi Rebecca,
> I suspect I know what you are trying to do and it involves diols,
> perhaps? My suggestion is to revise the model via by rescaling the 1-4
> electrostatic interactions and/or refitting the dihedral potentials to give
> you the conformational behavior that you are looking for. At least if you
> want to run in NAMD...
>
> --
> ======================================================================
> Jeffrey J. Potoff jpotoff_at_wayne.edu
> Professor and Director of Early Engineering Programs
> Department of Chemical Engineering and Materials Science
> Wayne State University 5050 Anthony Wayne Dr
> Detroit, MI 48202
> http://potoff1.eng.wayne.edu http://gomc.eng.wayne.edu
> ======================================================================
>
>
>
>
> On 11/5/2014 1:33 PM, Kenno Vanommeslaeghe wrote:
>
>> While the answer is in all likelihood "no", the question is poorly
>> formulated; I read it a few times over and I'm still confused about what
>> exactly you're looking for (and I work on force fields on a daily basis).
>> Do you mean "exceptions" instead of "interactions"? Also, if you want an
>> R^-12 repulsion without R^-6 attraction (which raises questions about the
>> rationale behind the force field), you also have to worry about whether
>> NAMD lets you specify them separately (I honestly don't know). Finally,
>> your "for example" link doesn't work; it likely relies on form data that is
>> not contained in the URL.
>>
>> On 11/05/2014 12:54 PM, Rebecca Lindsey wrote:
>>
>>> Dear All,
>>>
>>> Is there a way to include 1-5 (intramolecular) interactions in NAMD? As
>>> far as I understand, neither NBFIX nor NBTABLE can be used to accomplish
>>> this, as do not allow for a distinction between intra- and
>>> inter-molecular
>>> interactions.
>>>
>>> The repulsion term in question would be along the lines of: E_repel =
>>> a_repel/(r_ij)^12, as it is given by the TraPPE force field. (see, for
>>> example: http://www.chem.umn.edu/groups/siepmann/trappe/molname.php)
>>>
>>> Thanks in advance for your insights.
>>>
>>> --
>>> Rebecca K. Lindsey
>>> ----------------------------------------------------
>>> Ph. D. Candidate Website <https://sites.google.com/
>>> site/rebeccalindseycv/>
>>> University of Minnesota LinkedIn
>>> <http://www.linkedin.com/pub/rebecca-lindsey/17/b92/10>
>>> Twin Cities r.lindsey78_at_gmail.com <mailto:r.lindsey78_at_gmail.com>
>>> UMN Chemical Theory Center linds360_at_umn.edu <mailto:linds360_at_umn.edu>
>>> ----------------------------------------------------
>>>
>>
>>
>
>

-- 
Rebecca K. Lindsey
----------------------------------------------------
Ph. D. Candidate                         Website
<https://sites.google.com/site/rebeccalindseycv/>
University of Minnesota                     LinkedIn
<http://www.linkedin.com/pub/rebecca-lindsey/17/b92/10>
Twin Cities                  r.lindsey78_at_gmail.com
UMN Chemical Theory Center          linds360_at_umn.edu
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