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

Brian Smith bsmith at wehi.EDU.AU
Thu Aug 2 10:36:34 CEST 2007


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         
     2.93814e+03    4.04053e+01    7.73620e+01   -2.06722e+03    
    Coulomb (SR) Position Rest.      Potential    Kinetic En.   Total  
     1.08433e+03    1.74709e+01   -1.09928e+04    7.09543e+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?



Dr Brian J Smith
The Walter & Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville, Victoria 3050, Australia
Ph: +61 (0)3 9345 2687 Fax: +61 (0)3 9345 2686

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