[gmx-users] Explanation of contents of md.log file requested

[Mark Abraham]

Brian Smith wrote:
> Greetings,
> 
> 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?

short-range

> 2) Why is there no Bond term in the potential energy?

Have you constrained them to be constant?

Mark