Hi Jacob,
> On Jan 12, 2017, at 12:34 PM, Jacob Monroe <jimonroe.umail.ucsb.edu> wrote:
>
> Hi all,
>
> To clarify, the default behavior of leap in reading frcmod files or .dat parameter files is to read the information in the NONB section as the vdW radius (sigma*(2^(1/6))/2) and the energy well depth, correct?
>
That is correct.
> In the force field parameters provided in tutorial 27, "Material Systems Modeling Tutorial”, the interface_v1_5.dat file contains entries in the non-bonded terms that appear to simply be one half of the LJ sigma rather than the vdW radius. This is based on comparison with the paper here:
>
The interface_v1_5.dat file was created based on the “charmm27_interface_v1_5.prm” file released in INTERFACE_FF (v1.5) from
https://bionanostructures.com/interface-md/
> http://pubs.acs.org/doi/abs/10.1021/cm500365c
>
In this paper, the sigma is actually Rmin (comparing its equation 1 and the first equation in
https://en.wikipedia.org/wiki/Lennard-Jones_potential <
https://en.wikipedia.org/wiki/Lennard-Jones_potential>). So the parameters in interface_v1_5.dat should be fine.
> Just checking to make sure I’m interpreting this correctly, since I am very interested in using this force field.
>
> Thanks,
> Jacob
>
Hope it clarifies things.
Kind regards,
Pengfei
> ----------------------------------------
> Jacob I Monroe
> PhD Candidate
> Department of Chemical Engineering
> University of California - Santa Barbara
>
>
>
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Received on Thu Jan 12 2017 - 11:30:02 PST
