On 14/02/2012 12:55 PM, Juliette N. wrote:
On 13 February 2012 20:20, Mark Abraham <[email protected]
<mailto:[email protected]>> wrote:
On 14/02/2012 6:26 AM, Juliette N. wrote:
Hi all,
I have two simple question on in vacu calculations.
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).
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.
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.
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.
Mark
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?
3- Also why do we turn off PBC for in vacu runs?
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.
Mark
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