From: rocwhite168 (rocwhite168_at_163.com)
Date: Wed Nov 05 2014 - 14:55:05 CST
Is there really a LJ term between your 1,5 atoms? I thought there is
none which is why the special repulsion is needed.
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
> ----------------------------------------------------
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