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
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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 - 12:00:02 PST
