From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Mar 22 2017 - 13:09:02 CDT
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???
Director’s Postdoctoral Fellow
National Renewable Energy Laboratory
On Mar 22, 2017, at 11:55 AM, Wasut Pornpatcharapong <wpornpat_at_mail.ucsd.edu<mailto:wpornpat_at_mail.ucsd.edu>> wrote:
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,
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