[gmx-users] simulation in vacuum

Xavier Periole X.Periole at rug.nl
Wed Sep 17 16:15:45 CEST 2008

On Wed, 17 Sep 2008 16:14:08 +0200
  Thomas Schlesier <schlesi at uni-mainz.de> wrote:
>>/ Thank you.
> />/ But i have one last question:
> />/For epsilon_rf i use the relative permittivity of the medium. I simulate 
> />/vacuum so epsilon_rf would be 1?
> /GROMOS ff is not parameterized for vaccum simulations of the b-something
> version ... have look at the paper.
> So i should use ffG43b1 instead of the other GROMOS96 force fields?
That would be the right choice for the GROMOS43 ff series.
> In the GROMACS manual i found that the cut-off-distance must at least be 1.4 
>nm for the GROMOS96 force field.
Never believe what is written in a manual :))
It is always better to keep the values that are used for parameterization
(the one I gave you) when using a force field. The idea that bigger = better
does not work ... you change the balance of forces and thus the properties
of the force field.
> So can i use: type = cut-off; rlist = 1.4 and r_x = 1.7?
> (the problem is that the only reference i find for ffG43b1 is the GROMOS 
>manual, and that's not free avaible)
Any paper from van Gunsteren group or Alan Mark groujp (GROMOS developers)
would describe the simulation setup: no need of the manual for this.
> Thanks for an answer
> Thomas
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XAvier Periole - PhD

Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands

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