[gmx-users] zero cut offs
Mark.Abraham at anu.edu.au
Tue Feb 14 02:59:55 CET 2012
On 14/02/2012 12:55 PM, Juliette N. wrote:
> On 13 February 2012 20:20, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> 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.
> 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.
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