From: Jeffrey Potoff (jpotoffx_at_gmail.com)
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 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> >> ---------------------------------------------------- >
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