[gmx-users] Double entries in block structure--problem with SHAKE

tarak karmakar tarak20489 at gmail.com
Wed Nov 7 16:46:27 CET 2012

Dear All,

As I am facing the following problem while using SHAKE to constrain
some bonds, I have checked the mailing list but I think, this issue
has not been resolved. So if anyone knows the solution kindly inform

Program mdrun, VERSION 4.5.5
Source code file: invblock.c, line: 79

Fatal error:
Double entries in block structure. Item 5247 is in blocks 1371 and 1370
 Cannot make an unambiguous inverse block.

Actually I need to fix some of the ligand bonds along with the
covalent h-bonds (C-H, N-H, O-H etc.).
What do you suggest to use for this multiple constraining problem ?
Should I use SHAKE/LINCS for both type of bonds or anything else ?


More information about the gromacs.org_gmx-users mailing list