[gmx-users] constraints hbonds with 4.6

SebastianWaltz sebastian.waltz at physik.uni-freiburg.de
Mon May 21 11:13:46 CEST 2012

Hi all together,

I am testing the 4.6 dev version of gromacs with heterogeneous
acceleration (force field: amber99-ildn) on a 95 residue protein (all
atom model) in SPCE and run into major troubles using in the .mdp file
option constraints = hbonds with the default lincs parameters. The
system is exploding with the standard lincs warning (relative constraint
deviation after LINCS ......). Everything is working fine with the
option constraints = all-bonds or when I constrain all bonds with
hydrogen atoms manually in the .top file (which is a lot of effort).
Using gmxdump to search the .tpr file for the constraints I can't find
the bond constraints using the constraints = hbonds. Therefore I am
wondering if the very useful option is not included in the 4.6 version
of grompp or if there is something equal I don't know anything about.

Thank a lot for any response


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