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

Zoe Hall
Department of Chemistry
Oxford University

zoe.h...@chem.ox.ac.uk


-- 
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

Reply via email to