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On 14/02/2012 12:55 PM, Juliette N. wrote:
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<div class="gmail_quote">On 13 February 2012 20:20, 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="im">On 14/02/2012 6:26 AM, Juliette N. wrote:<br>
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Hi all,<br>
<br>
I have two simple question on in vacu calculations.<br>
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1- Say we start from rc=1, and go all the way to rc=0.1
then we say cut off has been reduced from 1 nm to 0.1 nm
meaning that atoms fall within 0.1 nm interact with each
other. Now when we set rc=0, why dont we consider this as
zero cutoff and that No interaction is cacluated for in
vacu simulation. When one sets r_vdw= 0, r_coulomb=0, why
people call this infinite cutoff and not zero cutoff (=no
nonboded interaction calculated).<br>
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Because it is defined that way. See manual section 7.3.9. In
theory, you could have another .mdp variable "cut-offs =
yes/no" to serve this purpose, but since the value zero serves
no useful purpose, it is used in the above way.
<div class="im">
<br>
Thank Mark. Can you please tell me rc=0 means all nonbonded
interaction are calculated (i.e. infinite cut off) or no
interaction is calculated (i.e. zero cut off; only bonded
interactions) ? I am asking this because I have seen on the
list that rc=0 is referred to as infinite cutoff.<br>
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Sorry, I was looking at nstlist=0 when I wrote my last answer.
However, if you read the whole section to which I referred you,
you'll see how to use infinite cut-offs.<br>
<br>
Mark<br>
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2-For calculation of heat of vaporisation why do we need
single molecule in vacu? why cant we leave cut off as in
liquid phase?<br>
<br>
3- Also why do we turn off PBC for in vacu runs?<br>
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Usually efficiency. Finding the nearest neighbours takes time,
and if there are few atoms at all (as is often the case with
vacuum simulations) it can be cheaper just to compute all the
interactions.<br>
<br>
Mark<br>
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