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From: Lambach, Lauren <lauren-lambach.uiowa.edu>

Date: Thu, 30 Jan 2020 22:25:28 +0000

Hi, I'm pretty new to Amber and I am trying to calculate the same forces that Amber gives in usefrcascoords using my own code given the positions of each atom, the charges, and the Lennard Jones A and B coefficients. For now, I am calculating the force from a single water molecule on a sodium ion so that I don't have to deal with any internal bond, angle, or dihedral forces. I am using F_VDW = ((12. * A / (r**13)) - (6. * B / (r**7))) * dr for the Van der Waals forces and F_ES = (Q1 * Q2 / r**2) * dr for the electrostatic forces, where dr is the derivative with the distance in the x, y, and z directions. I am also confused about how the cutoff distance works. My understanding is that when the water molecule and sodium ion are further apart than the cutoff, the forces should be 0, but that is not the case. Can someone please help shed some light one how Amber is calculating the forces on each atom for each frame?

Thank you,

Lauren

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Received on Thu Jan 30 2020 - 14:30:02 PST

Date: Thu, 30 Jan 2020 22:25:28 +0000

Hi, I'm pretty new to Amber and I am trying to calculate the same forces that Amber gives in usefrcascoords using my own code given the positions of each atom, the charges, and the Lennard Jones A and B coefficients. For now, I am calculating the force from a single water molecule on a sodium ion so that I don't have to deal with any internal bond, angle, or dihedral forces. I am using F_VDW = ((12. * A / (r**13)) - (6. * B / (r**7))) * dr for the Van der Waals forces and F_ES = (Q1 * Q2 / r**2) * dr for the electrostatic forces, where dr is the derivative with the distance in the x, y, and z directions. I am also confused about how the cutoff distance works. My understanding is that when the water molecule and sodium ion are further apart than the cutoff, the forces should be 0, but that is not the case. Can someone please help shed some light one how Amber is calculating the forces on each atom for each frame?

Thank you,

Lauren

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Thu Jan 30 2020 - 14:30:02 PST

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