From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Wed Mar 22 2017 - 14:17:09 CDT
Well, now I have to revise myself. Magnitude is always positive. The sign indicates whether or not the force is forward or backward along the vector direction.
But hopefully you can see how this reduces to a one-dimensional tabulation, as documented.
-- David J. Hardy, Ph.D. Theoretical and Computational Biophysics Beckman Institute, University of Illinois dhardy_at_ks.uiuc.edu http://www.ks.uiuc.edu/~dhardy/ > On Mar 22, 2017, at 2:09 PM, David Hardy <dhardy_at_ks.uiuc.edu> wrote: > > The functional form is for a distance-based pairwise potential and associated force. > > More precisely, the NAMD manual should read "force magnitude." > > Does that help? > > Dave > > -- > David J. Hardy, Ph.D. > Theoretical and Computational Biophysics > Beckman Institute, University of Illinois > dhardy_at_ks.uiuc.edu <mailto:dhardy_at_ks.uiuc.edu> > http://www.ks.uiuc.edu/~dhardy/ <http://www.ks.uiuc.edu/~dhardy/> >> On Mar 22, 2017, at 1:56 PM, Wasut Pornpatcharapong <wpornpat_at_mail.ucsd.edu <mailto:wpornpat_at_mail.ucsd.edu>> wrote: >> >> The parameters are actually the same for all dimensions, so I guess this would work? >> >> Sent from my iPhone >> >>> On Mar 22, 2017, at 11:09 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov <mailto:Joshua.Vermaas_at_nrel.gov>> wrote: >>> >>> Tabulated potentials take the place of LJ interactions, so its 1D in the sense that it ONLY depends on the vector between the two atoms in question (rij), but 3D in the sense that this naturally gives you forces along the x,y,z dimensions. Are your forces somehow different if the atoms are aligned along x rather than y or z??? >>> >>> Josh Vermaas >>> >>> Director’s Postdoctoral Fellow >>> National Renewable Energy Laboratory >>> joshua.vermaas_at_nrel.gov <mailto:joshua.vermaas_at_nrel.gov><mailto:joshua.vermaas_at_nrel.gov <mailto:joshua.vermaas_at_nrel.gov>> >>> >>> >>> >>> >>> On Mar 22, 2017, at 11:55 AM, Wasut Pornpatcharapong <wpornpat_at_mail.ucsd.edu <mailto:wpornpat_at_mail.ucsd.edu><mailto:wpornpat_at_mail.ucsd.edu <mailto:wpornpat_at_mail.ucsd.edu>>> wrote: >>> >>> Hello, >>> >>> I have read the manual and would like to use a tabulated external file for nonbonded interactions. I have found parameters in a paper and would like to use them. According to the manual, each line should have a format of, >>> >>> <table_spacing> <energy (kcal/mol)> <force (kcal/mol/A)> >>> >>> My question here is is this tabulated force or energy for 1D or 3D since there seem to be only one entry for force and energy in each row? The potential usually come in the form of r_ij (3D) so I need a clear idea before proceeding with simulation to make sure that I tabulate the nonbonded interactions correctly for force calculation in x,y,z dimensions. >>> >>> With kind regards, >>> >>> -Wasut (Khun) >>> >>> >>> >> >
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