[gmx-users] xx of the xxxx bonded interactions couldn't be calculated
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jun 7 09:19:55 CEST 2013
On 2013-06-07 04:12, Justin Lemkul wrote:
> On 6/6/13 10:00 PM, Badamkhatan wrote:
>> Dear GMX-users
>> Recently i got this error and note from my MD2 simulation. I'm solvating
>> 1-octanol to 1-octanol and calculating free energy differences. This
>> is the
>> last step of my calculation and previous steps are looking fine.
>> Basically i
>> followed Justin's free energy tutorial.
>> Here is
>> A list of missing interactions:
>> LJC Pairs NB of 210 missing 1
>> exclusions of 25308 missing 1
>> Molecule type '1-octanol'
>> the first 10 missing interactions, except for exclusions:
>> LJC Pairs NB atoms 3 25 global 3 25
>> Fatal error:
>> 2 of the 57736 bonded interactions could not be calculated because some
>> atoms involved moved further apart than the multi-body cut-off
>> distance (1
>> nm) or the two-body cut-off distance (1 nm), see option -rdd, for
>> pairs and
>> tabulated bonds also see option -ddcheck
>> Please help me and suggest any idea to solve this problem?
> Sounds like you're
It may also be the opposite, box shrinking under equilibration.
mdrun [options] -rdd 1.25
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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