Re: 1-5 Intramolecular repulsions

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Nov 05 2014 - 15:12:43 CST

On Wed, Nov 5, 2014 at 3:55 PM, rocwhite168 <rocwhite168_at_163.com> wrote:
> Is there really a LJ term between your 1,5 atoms? I thought there is
> none which is why the special repulsion is needed.

sure there is. with conventional force fields, all atoms outside the
exclusions are treated as regular non-bonded interactions. but TraPPE
is an "unconventional" force field. it is primarily used with MC.
there are other challenges for (parallel) MD codes, like rigid C-C
bonds, too.

axel.

>
> Roc
>
> On Wed, Nov 5, 2014 at 1:07 PM, Rebecca Lindsey <linds360_at_umn.edu> wrote:
>> 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
>> University of Minnesota LinkedIn
>> Twin Cities r.lindsey78_at_gmail.com
>> UMN Chemical Theory Center linds360_at_umn.edu
>> ----------------------------------------------------
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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