[gmx-users] Error: see option -rdd, for pairs and tabulated bonds also see option -ddcheck

[Mark Abraham]

Hi,

Very likely your run is blowing up from (long-time) instability - two atoms
have moved some crazy amount. You can probably confirm that from the time
series of some observables.

Mark

On Mon, Mar 9, 2015 at 12:54 PM, gromacs query <gromacsquery at gmail.com>
wrote:

> Hi All,
>
> I am doing CG membrane with protein. After running long simulation I am
> getting this error:
>
> Fatal error:
> 2 of the 13319 bonded interactions could not be calculated because some
> atoms involved moved further apart than the multi-body cut-off distance
> (1.4 nm) or the two-body cut-off distance (1.4 nm), see option -rdd, for
> pairs and tabulated bonds also see option -ddcheck
> For more information and tips for troubleshooting, please check the GROMACS
>
>
>
> I could not find this on google. Should I restart with something like -rdd
> 2 or so? I am just wondering how it will influence my overall calculations?
> I think it will reduce ns/day? or is there any serious energy related
> issues?
>
> Thanks,
> JIom
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