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On 16/02/2012 3:14 PM, Juliette N. wrote:
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cite="mid:CAGDQh4o_0SS70GgxKs=JTbOHcUthsgfn8djq8TXPsF1RdhKr=A@mail.gmail.com"
type="cite"><br>
<br>
<div class="gmail_quote">On 15 February 2012 23:05, Mark Abraham <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
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<div class="h5"> On 16/02/2012 2:08 PM, Juliette N. wrote:
<blockquote type="cite"><br>
<br>
<div class="gmail_quote">On 15 February 2012 21:00,
Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
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<div>On 16/02/2012 12:22 PM, Justin A. Lemkul
wrote:<br>
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style="margin:0pt 0pt 0pt
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<br>
Juliette N. wrote:<br>
<blockquote class="gmail_quote"
style="margin:0pt 0pt 0pt
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rgb(204,204,204);padding-left:1ex"> Hi all,<br>
<br>
I am trying to run simulation in vaccum
using the the changes shown below to the
usual mdp file.<br>
pbc = no<br>
<br>
;coulombtype = PME ;vdw-type
= Shift<br>
; Cut-offs<br>
rlist = 0 rcoulomb = 0<br>
rvdw = 0<br>
<br>
nstlist = 0
ns_type = simple<br>
<br>
Can anyone help me with some short questions
please?<br>
<br>
1- for pbc=no, I need to comment<br>
<br>
;coulombtype = PME ;vdw-type
= Shift<br>
so it defaults to vdw-type = Cut-off which
are not suitable algorithms. Is using cut
offs justified for in vacu runs?<br>
<br>
</blockquote>
<br>
Plain truncations in condensed-phase systems
lead to artifacts. Neither of those
conditions apply here, as you're using
infinite cutoffs.<br>
<br>
<blockquote class="gmail_quote"
style="margin:0pt 0pt 0pt
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rgb(204,204,204);padding-left:1ex"> <br>
2- I am not clear about using infinite
cutoffs. Why one refers to infinite cutoffs
when<br>
<br>
rlist = 0 rcoulomb = 0<br>
rvdw = 0 ?<br>
<br>
My understanding is that this settings means
zero cutoff i.e no interaction is
calculated. Why does this setting refer to
infinite rc?<br>
<br>
<br>
</blockquote>
<br>
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 ;)<br>
<br>
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.<br>
<br>
</blockquote>
<br>
</div>
Or read about pbc=no in manual section 3.4.9 like
I suggested Juliette do earlier this week...<br>
</blockquote>
<div><br>
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).</div>
</div>
</blockquote>
<br>
</div>
</div>
Sure, but reading the documentation is usually a better idea
than making assumptions :)<br>
<br>
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.
<div class="im"><br>
<br>
<blockquote type="cite">
<div class="gmail_quote">
<div>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? <br>
</div>
</div>
</blockquote>
<br>
</div>
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.<br>
</div>
</blockquote>
<div><br>
<br>
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.<br>
</div>
</div>
</blockquote>
<br>
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...<br>
<br>
Mark<br>
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