[gmx-users] zero cut offs

Juliette N. joojoojooon at gmail.com
Tue Feb 14 02:55:14 CET 2012

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