On 13 February 2012 20:20, Mark Abraham <[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. > >> >> 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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