[gmx-users] in vacu simulation

Juliette N. joojoojooon at gmail.com
Thu Feb 16 00:55:02 CET 2012

Hi all,

I am trying to run simulation in vaccum using the the changes shown below
to the usual mdp file.
pbc              =  no

;coulombtype         =  PME
;vdw-type            =  Shift

;        Cut-offs
rlist               =  0
rcoulomb     =  0
rvdw              =  0

nstlist             =  0
ns_type          =  simple

Can anyone help me with some short questions please?

1- for pbc=no, I need to comment

;coulombtype         =  PME
;vdw-type            =  Shift

so it defaults to vdw-type =  Cut-off which are not suitable algorithms. Is
using cut offs justified for in vacu runs?

2- I am not clear about using infinite cutoffs. Why one refers to infinite
cutoffs when

rlist               =  0
rcoulomb     =  0
rvdw              =  0     ?

My understanding is that this settings means zero cutoff i.e no interaction
is calculated. Why does this setting refer to infinite rc?

Thanks for your guidence,
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