[gmx-users] xx of the xxxx bonded interactions couldn't be calculated

[David van der Spoel]

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
>> Note:
>>   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
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up.
>
It may also be the opposite, box shrinking under equilibration.

Try:

mdrun [options] -rdd 1.25


> -Justin
>


-- 
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