[gmx-users] Simulations in vacuo
Mark.Abraham at anu.edu.au
Tue Jan 11 23:07:53 CET 2011
On 12/01/2011 2:29 AM, Zoe Hall wrote:
> 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.
vdwtype = cut-off
coulombtype = cut-off
and all the distance cut-offs to zero (which is treated as an infinite
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