[gmx-users] mdrun WARING and crash
jalemkul at vt.edu
Wed Feb 27 16:12:28 CET 2013
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
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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