[gmx-users] Simulations in vacuo

[Mark Abraham]

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 
cut-off)

Mark
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110112/974c35ca/attachment.html>