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.
-Justin
--
========================================
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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