[AMBER] What does the UVV file output for a LJ only system and why cant I recreate it?

From: Daniel Fowles <daniel.fowles.2014.uni.strath.ac.uk>
Date: Mon, 7 Jun 2021 11:59:26 +0000

Hi,

Iíve 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


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

677E3D2D19CB40DFA823CAD6A3101A29.png
(image/png attachment: 677E3D2D19CB40DFA823CAD6A3101A29.png)

DD03843984994C1C80A1E97B861ACB01.png
(image/png attachment: DD03843984994C1C80A1E97B861ACB01.png)

DB9019300A074F32B8EF9270DB7D9ACC.png
(image/png attachment: DB9019300A074F32B8EF9270DB7D9ACC.png)

Received on Mon Jun 07 2021 - 05:00:03 PDT
Custom Search