# NAMDenergy

From: Francesco Coppola (fcoppo3_at_uic.edu)
Date: Mon May 16 2022 - 13:41:19 CDT

Dear community,

I have a system where I have a protein and a molecule interacting with it.
I select them individually in selection 1 and selection 2. So I calculate
VDW, Electrostatic, and not bond.
I have a question about the "Show only force projection" (-projforce)
option. In particular, what is its use?

"This flag is only meaningful when combined with keepforce. When specified,
the output forces will be the projection of the total forces onto the
vector between the center of mass of the two selections. In this case the
forces are signed quantities; a negative force is attractive and a positive
force repulsive. "

Can I have the same conclusions with the total value that I get without the
projection? Negative attraction, positive repulsion. If so, then when is it
useful to calculate this projection instead?

Here is an excerpt of a few frames (the column with ....Force should be
where there is the projection):

Frame Time Elec VdW Nonbond Total
VdWForce ElecForce TotalForce
0 0 -3245.88 +173.494 -3072.38
-3072.38 +811.377 -213.527 +597.85
1 1 -7762.9 -123.821 -7886.72
-7886.72 +10.5077 -297.125 -286.618
2 2 -7340.49 -108.611 -7449.1
-7449.1 +29.166 -309.366 -280.2
3 3 -7074.83 -116.162 -7190.99
-7190.99 +49.8759 -330.87 -280.994
4 4 -7336.34 -123.698 -7460.03
-7460.03 +27.4836 -345.997 -318.514
5 5 -7390.09 -110.634 -7500.72
-7500.72 +2.1968 -279.203 -277.006

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