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From: William Marquardt <williamkmarquardt.gmail.com>

Date: Fri, 13 Oct 2017 13:24:46 -0500

Greetings AMBER users!

This is my first posting, so please let me know what specifics I should be

providing when asking questions:

I've run a short simulation of azide anion in vacuo, and am having a bear

of a time generating force vectors that match what the .mdfrc output reads.

dt=0.001, and I am printing forces and coordinates each timestep for the

duration of this short NVE simulation. Since there is only one azide, and

I know the spring constants for its bending and stretching motion, I should

be able to calculate the total force acting on it by multiplying the spring

constant by the displacement from equilibrium in the relevant degree of

freedom (delta_x for the N1-N2 and N2-N3 bond, delta_theta for the bending

spring constant), and multiplying it by a unit vector in the proper

direction. For the stretch, that is simple enough - it's just the N1-N2

and N2-N3 bond vector and their negative for each atom.

The bending vector is a little trickier, but exist published expressions

for the unit vector in Cartesian coordinates.

I am consistently finding that my results, however, are not matching what's

in the .mdfrc file, even if they wind up being similar in magnitude.

My question, then, is this:

What exactly is in the .mdfrc file? It was my understanding that it's the

force calculated for each atom, which determines its coordinates in the

next frame. I would expect it does not include any nonbonded interactions,

since it's 12A from the edges of my box. I should be able to calculate

what's in the .mdfrc from just the spring equations. Is there an

additional term I should be considering? I'd thought it might be that

there is a difference in origin for my forces and coordinates, but the norm

of my calculated forces is also slightly off as compared to the force

vector in the .mdfrc file.

For context, I am looking to remove the intramolecular forces acting on N1,

N2, and N3 so that I can project the intermolecular forces acting on the

azide along the antisymmetric stretch axis for a spectroscopic calculation.

Thanks for your consideration,

Will

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Received on Fri Oct 13 2017 - 11:30:02 PDT

Date: Fri, 13 Oct 2017 13:24:46 -0500

Greetings AMBER users!

This is my first posting, so please let me know what specifics I should be

providing when asking questions:

I've run a short simulation of azide anion in vacuo, and am having a bear

of a time generating force vectors that match what the .mdfrc output reads.

dt=0.001, and I am printing forces and coordinates each timestep for the

duration of this short NVE simulation. Since there is only one azide, and

I know the spring constants for its bending and stretching motion, I should

be able to calculate the total force acting on it by multiplying the spring

constant by the displacement from equilibrium in the relevant degree of

freedom (delta_x for the N1-N2 and N2-N3 bond, delta_theta for the bending

spring constant), and multiplying it by a unit vector in the proper

direction. For the stretch, that is simple enough - it's just the N1-N2

and N2-N3 bond vector and their negative for each atom.

The bending vector is a little trickier, but exist published expressions

for the unit vector in Cartesian coordinates.

I am consistently finding that my results, however, are not matching what's

in the .mdfrc file, even if they wind up being similar in magnitude.

My question, then, is this:

What exactly is in the .mdfrc file? It was my understanding that it's the

force calculated for each atom, which determines its coordinates in the

next frame. I would expect it does not include any nonbonded interactions,

since it's 12A from the edges of my box. I should be able to calculate

what's in the .mdfrc from just the spring equations. Is there an

additional term I should be considering? I'd thought it might be that

there is a difference in origin for my forces and coordinates, but the norm

of my calculated forces is also slightly off as compared to the force

vector in the .mdfrc file.

For context, I am looking to remove the intramolecular forces acting on N1,

N2, and N3 so that I can project the intermolecular forces acting on the

azide along the antisymmetric stretch axis for a spectroscopic calculation.

Thanks for your consideration,

Will

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

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

Received on Fri Oct 13 2017 - 11:30:02 PDT

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