On 16/02/2012 3:14 PM, Juliette N. wrote:
On 15 February 2012 23:05, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 16/02/2012 2:08 PM, Juliette N. wrote:
On 15 February 2012 21:00, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
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...
Thanks Justin and Mark. I think you meant 7.3.9 which I did when
you referred me to that. My problem was that I did not expect
rc=0 is *just defined* as infinite cutoff in gromacs. To me rc=0
looked more equivalent to no interaction than infinite cutff off
(all interactions).
Sure, but reading the documentation is usually a better idea than
making assumptions :)
The underlying reason for this behaviour is that it is much easier
for the person writing the code to have one parameter that
occasionally has a "special" meaning when it takes a nonsense
value (like rc<=0) then it is to have a slew of parameters that
have to be managed when they are input (and checked, and
documented) and then possibly passed through a cascade of
functions (lots of bureaucracy and chances to make errors) before
they are used. The alternative costs the programmer more time. In
an ideal world there would be an infinite amount of such time, but
given the amount most people are prepared to pay for scientific
software, that time is severely limited.
And also I dont see why do we need to change rc to infinite. I
mean if force fields dictate cutoffs based on a distance where
nonbonded interactions are close enough to zero (negligible),
what purpose use of infinite cutoff serve?
Efficiency, like I said in the first post in this thread. Given
that your force field was parametrized with given cut-offs for the
condensed phase, to what purpose do you wish to calculate in
vacuo? The perturbation from calculating in vacuo will be much
larger than the perturbation from the use of infinite cut-offs.
Thank you. I am looking at potential of a single molecule in vacu for
heat of vap purposes at different temperatures by changing ref_temp
and gen_temp for each run.
So it's much more bureaucracy every nstlist>0 steps to take your N atoms
and look at their distance from the other N-1 atoms and make lists of
which ones are inside rc than it is to just compute them all every step
and know that if they're further than rc then the effect is tiny. For
small enough N, the later is guaranteed to be faster...
Mark
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