[gmx-users] gas-phase protein simulation

[David van der Spoel]

yes all cutoffs 0 and epsilon_rf 1 and nstlist 0 as well.

Toodle pip!

On Nov 30, 2011, at 8:39 PM, "Shi, Huilin" <huilshi at imail.iu.edu> wrote:

> Hi,
> 
> I would like to run a gas-phase protein simulation (with charge state of  +8). 
> I have read this paper : Biochemistry, 2007, 47, 933-945.
> 
> In the method section of vaccum simulation, it is said
>  "For the remaining parameters, the same settings were used as in the water simulations, 
> except that the periodic boundary conditions were turned off and no cutoffs whatsoever were used."
> 
> I am confused about "no cutoffs whatsoever were used".
> Does that mean setting all the cutoffs to be zero?
> In the md.mdp file, can I use the following
> 
> "; NEIGHBORSEARCHING PARAMETERS
> nstlist                  = 0
> ns-type                  = simple
> pbc                      = no
> rlist                    = 0
> 
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype              = cut-off
> rcoulomb                 = 0
> epsilon_rf               = 78
> epsilon_r                = 1
> vdw-type                 = Cut-off
> rvdw                     = 0"
> 
> Do I need to set rcoulomb/rvdw to zero or some other number?
> 
> Thank you.
> 
> 
> Huilin
> -- 
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111130/2ee9ef4e/attachment.html>