Re: 1-5 Intramolecular repulsions

From: Jeffrey Potoff (
Date: Wed Nov 05 2014 - 12:51:02 CST

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               
Professor and Director of Early Engineering Programs
Department of Chemical Engineering and Materials Science
Wayne State University			  5050 Anthony Wayne Dr
Detroit, MI 48202    
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:
>> Thanks in advance for your insights.
>> -- 
>> Rebecca K. Lindsey
>> ----------------------------------------------------
>> Ph. D. Candidate Website 
>> <>
>> University of Minnesota LinkedIn
>> <>
>> Twin Cities <>
>> UMN Chemical Theory Center <>
>> ----------------------------------------------------

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