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Issue created by Paul Bauer@acmnpvMaintainer

[ intermolecular_interactions ] with [ distance_restraints ] / [ bonds ] not working - Redmine #2953

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 3cbf2eb5 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 9e4323b6 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