[gmx-users] stochastic dynamics parameters

Berk Hess gmx3 at hotmail.com
Mon Jul 21 12:20:01 CEST 2003

>Hi, All:
>I did stochastic dynamics of protein GB1 with
>G9643a1 FF and published gmx3.0.5. When I set the
>epsilon_r to be 1, the Coulomb (SR) energy of the
>starting conformation which was optimised by EM
>is around -9000 kj/mol. This value is much higher than what I get from 
>Gromos package with every setting
>the same. I am not sure whether I set the parameters
>correctly in my mdp so I put them here. Any hints
>will be sincerely appreciated!

This problem has nothing to do with stochastic dynamics.

My guess would be that the Gromos package reports the sum
of the Gromacs Coulomb (SR) and the Coul-14 terms.
Check if this sum does correspond to the Gromos number.


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