On 16/02/2012 12:22 PM, Justin A. Lemkul wrote:
Juliette N. wrote:
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?
Plain truncations in condensed-phase systems lead to artifacts.
Neither of those conditions apply here, as you're using infinite cutoffs.
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?
That's the way the code works. There are various parameters that can
be set to -1, for instance, and that doesn't mean quantities are
calculated every -1 steps ;)
Setting cutoffs to zero in this manner mean *all* interactions are
calculated, not none. Prove it to yourself with a zero-step MD run.
The nonbonded energy terms will not be zero, as they would in the case
that no interactions would be calculated.
Or read about pbc=no in manual section 3.4.9 like I suggested Juliette
do earlier this week...
Mark
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