Questions and problems?

Units

I'm wondering why atomic charges in the topology files are calculated as (atomic charge in the all_amino.in) * 18.2223.

Dave Case: If you measure charge in units of the electron charge, and distance in Angstroms (as is done in amber), then an electrostatic energy looks like: 

    E (kcal/mol) =  332 * q1*q2/r
where q1 and q2 are charges and r is a distance. The square root of 332 is 18.2; hence, to save the multiplication by 332 all of the time, the charges are modified by 18.2, so that 
     E (kcal/mol) =  (18.2*q1) * (18.2*q2) / r
I have been trying to calculate kinetic energies from the velocities in the restrt files of minmd. Comparing the results with the value in the corresponding mdinfo file shows a completely different kinetic energy both in the numbers and in the order of magnitude, which is about 1000 times off. I assume that the kinetic energy in the mdinfo file is in kcal/mol and I would like to know what the units for the velocity components in the restrt file are. I thought that they were Angstrom/picosecond, but considering what they should be on average for a certain temperature, the velocities in the restrt seem to be 10-100 times smaller.

Amber internally uses lengths in angstroms, masses in atomic mass units, and energies in kcal/mol. This means that the unit of time is 1/20.455 ps. Since the set of units is internally consistent, you should be able to compute the kinetic energy in the "normal" fashion: 

   KE(in kcal/mol) = 1/2 sum mv**2
where the masses are in amu and the velocities are from the program.

Note, however, that the velocities stored in the restart file are the velocities at a time 0.5(dt) before the time of coordinate (since a "leap-frog" integration scheme is being used. When amber actually prints kinetic energies, it estimates the velocities at the current time [by averaging those at t - 0.5(dt) and t + 0.5(dt)]. So your kinetic energies won't exactly match those printed unless you do something equivalent.

VDW parameters: R* is in Angstroms, epsilon in kcal/mol.