[gmx-users] Re: stochastic dynamics parameters (Berk Hess)

Fan Hao f.Hao at chem.rug.nl
Tue Jul 22 10:28:00 CEST 2003

> Message: 1
> From: "Berk Hess" <gmx3 at hotmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] stochastic dynamics parameters
> Date: Mon, 21 Jul 2003 12:18:58 +0200
> Reply-To: gmx-users at gromacs.org
> >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.
> Berk.

Yes, in Gromos package, it only gives summation of Coulomb (SR) and
Coul-14. The summation of the two terms in Gromacs give almost
the same value. Thanks a lot!



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