[gmx-users] Simulations in vacuo

Zoe Hall zoe.hall at chem.ox.ac.uk
Tue Jan 11 16:29:01 CET 2011

Hi gmx-users,

I am trying to set up a simulation of a large protein in vacuo using the OPLS-AA forcefield, with conditions based on Patriksson et. al (Biochemistry 2007, 46 p933).  Basically after energy minimisation, the protein is run for 10ps in vacuum with constant temperature at 300K. This is followed by the full production run of 10ns with temperature and pressure coupling turned off, H bonds are constrained using SHAKE with tolerance 0.001. For vacuum conditions, the periodic boundary conditions are turned off, and no cut-offs are used whatsoever.

I am not sure, however, what is the appropriate choice for "coulombtype" and other electrostatic parameters for vacuum simulations. I have set "epsilon_r" to 2, as this seems to be an accepted value for proteins but if anyone has comments on this, I would appreciate it.

Thanks very much,


Zoe Hall
Department of Chemistry
Oxford University

zoe.hall at chem.ox.ac.uk

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