[gmx-users] zero cut offs

[Mark Abraham]

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.

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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