[gmx-users] Problems with periodic syatems

[susanta haldar]

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.