[gmx-users] Explanation of contents of md.log file requested
Mark.Abraham at anu.edu.au
Thu Aug 2 11:48:03 CEST 2007
Brian Smith wrote:
> A summary of different energy contributions is written to the the md.log
> file during an MD calculation. Below is an extract,...
> Energies (kJ/mol)
> Angle Ryckaert-Bell. LJ-14 Coulomb-14 LJ (SR)
> 2.93814e+03 4.04053e+01 7.73620e+01 -2.06722e+03 -1.30833e+04
> Coulomb (SR) Position Rest. Potential Kinetic En. Total Energy
> 1.08433e+03 1.74709e+01 -1.09928e+04 7.09543e+03 -3.89738e+03
> Temperature Pressure (bar)
> 3.03856e+02 8.52321e+02
> The Potential energy is simply the sum of Angle, Ryckaert-Bell, LJ-14,
> Coulomb(14), LJ(SR), Coulomb(SR) and Position Rest. energies.
> I have two questions,...
> 1) What does the acronym 'SR' stand for?
> 2) Why is there no Bond term in the potential energy?
Have you constrained them to be constant?
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