[gmx-users] dppc benchmark forcefield

[Erik Lindahl]

Pedro Alexandre Lapido Loureiro wrote:

>Hello,
>
>I am using the forcefield attached to dppc1024 benchmark for my own system.
>It is from Berger (Biophys. J. 72,2002-2013,1997) but with two main exceptions:
>
>  LC2    14.02700       0.000       A   0.70067E-02   0.24845E-04
> LC2O    14.02700       0.000       A   0.59496E-02   0.17914E-04
>
>According to Berger, should be:
>
>  LC2    14.02700       0.000       A   0.85953E-02   0.30478E-04
> LC2O    14.02700       0.000       A   0.72985E-02   0.21975E-04
>
>Besides, the LJ and Coulomb 1-4 interactions should have been scaled with fudge
>factors 0.25 and 0.5, respectively.
>
>Forgive me for this (another!) boring question ...
>

Hi Pedro,

You are right about the fudge factor - we must have missed that when we 
updated the benchmark for 3.1.
(The fudge factor used to be given in the mdp file instead); I'll try to 
remember to fix it for the next release.

The oxygen parameters are more difficult; I have a vague memory of 
checking Oliver (Berger)'s parameters
and finding that the correct OPLS parameters were very slightly 
different. It doesn't make a huge difference,
but if it is important I would recommend checking OPLS.

Cheers,

Erik