[gmx-users] Error in mdrun

Hanin Omar hanin_omar85 at yahoo.com
Wed May 8 18:44:55 CEST 2019

Hi allI am trying to run md simulation of a 83 residue protein with AMBER99SB-ILDN protein forcefield and TIP3P water model, i am adding orientation restraint to my protein alone however when i run NVT equlibration i get this errorFatal error:
Found 5384 copies of a molecule with orientation restrains while the current
code only supports a single copy. If you want to ensemble average, run
multiple copies of the system using the multi-sim feature of mdrun.

To my understanding this means that gromacs is applying the RDC restraints on all water molecule which is weird cause in my topology file i added the restraint file before including the water topology like this:; Include RDC restraint file
#include "RDC-restraint.itp"

; Include water topology
#include "amber99sb-ildn.ff/tip3p.itp" also in my mdp file i have this section:;Options for orientation restraint
orire                    = yes
orire-fc                 = 1   ; Orientation restraints force constant
orire-tau                = 0   ; Turn off time averaging
orire-fitgrp             = backbone 

is their something i need to add so that gromacs apply the rdc restraint only on the protein.i really appreciate the helpThank you 
Hanin OMar

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