[gmx-users] gas-phase protein simulation

[Justin A. Lemkul]

Shi, Huilin 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?
> 

Your settings are correct, although epsilon_r and epsilon_rf are unnecessary.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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