Date: Mon, 7 Jun 2021 11:59:26 +0000
Hi,
I’ve created a system with two identical atoms These two atoms are represented by LJ sigma (5.05) and epsilon (0.85) values only. I can output a uvv file showing the interactions between these two atoms with respect to the distance between them. As these atoms are only made up of LJ parameters, the energy at any distance should be equal to the vdW energy calculated using any of the three formula given in the amber manual:
[V_(LJ_1)=4e[(s/r)^12-(s/r)^6 ]]
[V_(LJ_2)=4e[1/4 (r_0/r)^12-1/2 (r_0/r)^6 ]]
[V_(LJ_3)=((er_0^12 ))/r^12 -((2er_0^6 ))/r^6]
These three formula all give the same energy values, but they are still off the value given in the uvv file. Am i using the correct formula, or is there something I have missed out? See below a portion of the uvv output.
Distance energy
4.50E+00
6.80E+00
4.53E+00
6.14E+00
4.55E+00
5.54E+00
4.58E+00
4.99E+00
4.60E+00
4.48E+00
4.63E+00
4.02E+00
4.65E+00
3.59E+00
4.68E+00
3.19E+00
4.70E+00
2.83E+00
4.73E+00
2.50E+00
4.75E+00
2.19E+00
4.78E+00
1.91E+00
4.80E+00
1.65E+00
4.83E+00
1.41E+00
4.85E+00
1.20E+00
4.88E+00
9.96E-01
4.90E+00
8.13E-01
4.93E+00
6.46E-01
4.95E+00
4.93E-01
4.98E+00
3.53E-01
5.00E+00
2.25E-01
5.03E+00
1.09E-01
5.05E+00
2.72E-03
5.08E+00
-9.40E-02
5.10E+00
-1.82E-01
5.13E+00
-2.62E-01
5.15E+00
-3.34E-01
5.18E+00
-3.99E-01
5.20E+00
-4.58E-01
5.23E+00
-5.11E-01
5.25E+00
-5.59E-01
5.28E+00
-6.02E-01
5.30E+00
-6.40E-01
5.33E+00
-6.74E-01
5.35E+00
-7.04E-01
5.38E+00
-7.30E-01
5.40E+00
-7.53E-01
5.43E+00
-7.73E-01
5.45E+00
-7.90E-01
5.48E+00
-8.05E-01
5.50E+00
-8.17E-01
5.53E+00
-8.27E-01
5.55E+00
-8.35E-01
5.58E+00
-8.41E-01
5.60E+00
-8.46E-01
5.63E+00
-8.49E-01
5.65E+00
-8.50E-01
5.68E+00
-8.51E-01
5.70E+00
-8.50E-01
5.73E+00
-8.48E-01
5.75E+00
-8.45E-01
5.78E+00
-8.41E-01
5.80E+00
-8.37E-01
5.83E+00
-8.31E-01
5.85E+00
-8.26E-01
5.88E+00
-8.19E-01
5.90E+00
-8.12E-01
5.93E+00
-8.05E-01
5.95E+00
-7.97E-01
5.98E+00
-7.88E-01
6.00E+00
-7.80E-01
6.03E+00
-7.71E-01
6.05E+00
-7.62E-01
6.08E+00
-7.53E-01
6.10E+00
-7.43E-01
6.13E+00
-7.33E-01
6.15E+00
-7.24E-01
6.18E+00
-7.14E-01
6.20E+00
-7.04E-01
6.23E+00
-6.94E-01
6.25E+00
-6.84E-01
6.28E+00
-6.74E-01
6.30E+00
-6.64E-01
6.33E+00
-6.53E-01
6.35E+00
-6.43E-01
6.38E+00
-6.33E-01
6.40E+00
-6.23E-01
6.43E+00
-6.13E-01
6.45E+00
-6.04E-01
6.48E+00
-5.94E-01
6.50E+00
-5.84E-01
6.53E+00
-5.74E-01
6.55E+00
-5.65E-01
6.58E+00
-5.55E-01
6.60E+00
-5.46E-01
6.63E+00
-5.37E-01
6.65E+00
-5.28E-01
6.68E+00
-5.19E-01
6.70E+00
-5.10E-01
6.73E+00
-5.01E-01
6.75E+00
-4.92E-01
6.78E+00
-4.84E-01
6.80E+00
-4.75E-01
6.83E+00
-4.67E-01
6.85E+00
-4.59E-01
6.88E+00
-4.51E-01
6.90E+00
-4.43E-01
6.93E+00
-4.35E-01
6.95E+00
-4.27E-01
6.98E+00
-4.20E-01
7.00E+00
-4.12E-01
Any help would be much appreciated,
Thanks
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