[gmx-users] Re: protein unfolding, gromacs parametrisation

Aina Quintilla aina.quintilla at int.fzk.de
Fri Mar 18 15:20:28 CET 2005

dear gromacs´ users,

i try to do a simulation of a 1l2y protein..  

the protein is anyway unfolding with the suggested parameters´ choice : 

> rlist = 0.8
> rcoulomb = 1.4
> rvdw = 1.4

> This si the way Gromos force field have been parametrized.
> may be nstlist = 5

i do not understand yet what it´s meant by parametrized.. could somebody give 
me some reference where i can read about it? is it written in the user´s 
guide how is gromos force field parrametrized?

anyway, i would be very thankful if anyone could give any suggestion 
concerning the unfolding of the protein (1l2y) after an energy minimisation 
and a short position restraint run..

thank you

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