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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
