Hi Jacob,
No problem. It is easy to overlook that. Good luck with your research!
Kind regards,
Pengfei
> On Jan 12, 2017, at 1:53 PM, Jacob Monroe <jimonroe.umail.ucsb.edu> wrote:
>
> Thanks, Pengfei! Sorry for the confusion. I should have checked the equation more carefully.
>
> Jacob
>
> On Jan 12, 2017, at 11:11 AM, Pengfei Li <ambermailpengfei.gmail.com<mailto:ambermailpengfei.gmail.com>> wrote:
>
> Hi Jacob,
>
> On Jan 12, 2017, at 12:34 PM, Jacob Monroe <jimonroe.umail.ucsb.edu<mailto: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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> ----------------------------------------
> Jacob I Monroe
> PhD Candidate
> Department of Chemical Engineering
> University of California - Santa Barbara
>
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Received on Thu Jan 12 2017 - 12:30:03 PST
