[gmx-users] Error in mdrun

Harimuthu mmddharimuthu at gmail.com
Fri Oct 21 19:54:37 CEST 2016


hello sir

While running the protein in water energy minimisation
gmx mdrun -v -deffnm em
an error is occurred as follows

Program gmx mdrun, VERSION 5.1.2
Source code file:
/build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: 555

Fatal error:

step 14: Water molecule starting at atom 8686 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


in that i searched the error in input file which was in 8686 atom and found
a error in coordinate value of water it was as
ATOM   8686  OW  SOL  1551       0.823  30.858  10.228  1.00
0.00
ATOM   8687  HW1 SOL  1551       0.825  31.173  11.177  1.00
0.00
ATOM   8688  HW2 SOL  1551      95.631  30.777   9.906  1.00  0.00

in this the third atom X coordinate is 95.631 and i changed it into 0.631 i
dont know whether to relible or no, if i do potential graph it is good to
see, so can anyone help me in solving this problem
With regards
Harimuthu


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