Archive from user: Eiso AB see also https://mailman-1.sys.kth.se/pipermail/gromacs.org\_gmx-users/2019-May/125277.html I’m trying to implement NMR (noe) and Hbond restraints between protein, ligand and 2 SOL molecules using \[ distance\_restraints \] (or \[ bonds \]) \[ intermolecular\_interactions \] \[ distance\_restraints \] ; ai aj ftype label rtype low up0 up1 weight ; & source 1607 5241 1 18 1 0.5680 0.5680 0.6384 1 ; \# 120 leu hd1\# 411 lig h09 5.68 \# 4.74 0.94 1608 5241 1 18 1 0.5680 0.5680 0.6384 1 ; \# 1609 5241 1 18 1 0.5680 0.5680 0.6384 1 ; \# …etc \[ bonds \] 5261 5569 10 0.2800 0.3200 10.4333 1 ; \# 411 lig o19 501 sol ow 3.00 etc… With both \[ bonds \] and \[ distance\_restraints \] the mdrun starts, but non of the restraints seem to be active - waters just fly away etc. Also for \[ distance\_restraints \] no Dist. Res energy is printed in the log file - unlike when they intramolecular and defined with the appropriate molecule section. Not sure if it is related, but when I run gmx\_disre I get the following error: %>gmx disre -s md\_0\_10.tpr -f md\_0\_10.xtc ------------------------------------------------------------------------ Program: gmx disre, version 2019-beta1 Source file: src/gromacs/listed-forces/disre.cpp (line 174) Function: init\_disres(FILE**, const gmx\_mtop\_t**, t\_inputrec**, const t\_commrec**, const gmx\_multisim\_t**, t\_fcdata**, t\_state\*, gmx\_bool)::\_\_lambda0 Assertion failed: Condition: type\_max - type\_min + 1 == dd->nres All distance restraint parameter entries in the topology should be consecutive and %>gmx nmr -s md\_0\_10.tpr -f md\_0\_10.edr -viol viol.xvg yields: ------------------------------------------------------------------------ Program: gmx nmr, version 2019-beta1 Source file: src/gromacs/commandline/filenm.cpp (line 88) Function: opt2fn(const char**, int, const t\_filenm**)::\_\_lambda1 Assertion failed: Condition: false opt2fn should be called with a valid option If needed I can produce a toy example but will have to make one up since I can’t share the files I’m working on -let me know. Eiso *(from redmine: issue id 2953, created on 2019-05-14 by gmxdefault, closed on 2019-05-29)* * Changesets: * Revision 3cbf2eb5c8c918130de553df77989af8708218fc by Berk Hess on 2019-05-29T15:59:54Z: ``` Fix missing intermolecular interactions with DD When running with domain decomposition, all intermolecular interactions (when present) were ignored. Fixes #2953 Change-Id: I98783f4175b40fdfa6ad035323e0897e8caaee5c ``` * Revision 9e4323b6cbd20ca0c3f9dd71a8405d1a0397f66d by Berk Hess on 2019-08-02T14:50:54Z: ``` Made gmx disre work with non-consecutively labeled restraints gmx disre assumed restraint were consecutively labeled starting at 0. Refs #2953 Change-Id: I7d9c14d43854c88cb1cdec89fc297c64cbea8783 ``` * Uploads: * [topol.top](/uploads/f70f518a19d98558ca046361f60ba88c/topol.top) * [conf.gro](/uploads/f31b4fb29eb2257c0053cf4ff61451d0/conf.gro) * [grompp.mdp](/uploads/873ad552432a49264bd0834f91febc24/grompp.mdp) * [test-1.log](/uploads/7299f908798b08e08e52d489742f823d/test-1.log) mdrun log file for run that works ok. * [test-2.log](/uploads/197ca6bb16543dfca5cd595730c447ef/test-2.log) mdrun log file for broken run