[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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