[gmx-users] mdrun WARING and crash

[Justin Lemkul]

On 2/27/13 9:43 AM, L.Liu at utwente.nl wrote:
> Dear Justin,
>
> Thank you for your reply. I have some other questions,
>
> 1) Is it allowed to set nrexcl=0 in topology file in order to make every coarse-grained particles interact with each.
>

Are there bonded interactions?  If so, such an exclusion setup doesn't make much 
sense.

> 2) If it is allowed, then in [pairs] section, do I need to list all the pairs?
> For example, a linear chain with 10 beads:
> [ pairs ]
> 1 2
> 1 3
> 1 4
> 1 5
> ......
> 2 3
> 2 4
> ......
> 9 10
>
> or it can recognize the 1-5 1-6 or above automatically.
>

Well, with nrexcl=0, then all nonbonded interactions will be calculated, but 
pairs are usually used to modify the default interactions.  Please see the very 
recent, extensive discussions in the list archive on this topic.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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