[gmx-users] Problems with periodic syatems

[Mark Abraham]

Much more likely your initial conditions are unsuited for applying
periodicity, such as overlapping atoms e.g. from insufficient extra space
around the atoms at the edges of the box.

And next time, please link to "I saw somewhere that..." (coz that was
probably wrong or out of context).

Mark


On Mon, Mar 3, 2014 at 5:14 PM, susanta haldar <susantahaldar at gmail.com>wrote:

> Hi all,
>
>    I am having trouble to simulate the periodic system with the gmxV-4.6.3.
> I am running the simulation in GPU's. Every time there has a problem with
> the bonded interaction like that given below-
> ###############################################################
> Program mdrun_omp, VERSION 4.6.3
> Source code file:
>
> /usr/local/programs/gromacs/gromacs-4.6.3/src/gromacs-4.6.3/src/mdlib/domdec_top.c,
> line: 393
>
> Fatal error:
> 1 of the 103102 bonded interactions could not be calculated because some
> atoms involved moved further apart than the multi-body cut-off dist
> ance (0.528 nm) or the two-body cut-off distance (1.056 nm), see option
> -rdd, for pairs and tabulated bonds also see option -ddcheck
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> #################################################################
>
> But when I was running without a periodic system, it was okay. Could
> somebody please help me to get rid of this. The problem might come due the
> domain decomposition problem. I saw somewhere that the domain decomposition
> algorithm doesn't work properly for the periodic systems.
>
> thanks in advance.
>
> --
> Susanta Haldar
> Institute of Organic Chemistry and Biochemistry
> Academy of Sciences of the Czech Republic.
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