<br><br><div class="gmail_quote">On 15 February 2012 23:05, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><div><div></div><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 href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>On 16/02/2012 12:22 PM, Justin A. Lemkul
wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
<br>
Juliette N. wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid 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 0.8ex;border-left:1px solid 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><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000"><font color="#888888">
<br>
Mark<br>
</font></div>
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