Group cut-off scheme grompp error: Could not find energy term named 'Xi-0-Protein_LIG' - Redmine #2301
Archive from user: Yu Du
I want to choose the last N frames from nvt-normal2.trr as starting coordinates and velocities.
gmx grompp -quiet -f nvt.mdp -c nvt-normal2.gro -t nvt-normal2.trr -time 8 -e nvt-normal2.edr -p topol.top -n index.ndx -o nvt-8.tpr
I didn’t change the thermostat and grompp errors are shown below.
NOTE 1 [file nvt.mdp]:
The group cutoff scheme is deprecated since GROMACS 5.0 and will be
removed in a future release when all interaction forms are supported
for
the verlet scheme. The verlet scheme already scales better, and it is
compatible with GPUs and other accelerators.
Setting the LD random seed to –1655106643
Generated 2628 of the 2628 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2628 of the 2628 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘LIG’
turning H bonds into constraints…
Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
turning H bonds into constraints…
Excluding 2 bonded neighbours molecule type ‘SOL’
turning H bonds into constraints…
Excluding 1 bonded neighbours molecule type ‘NA’
turning H bonds into constraints…
Number of degrees of freedom in T-Coupling group Protein_LIG is
15018.52
Number of degrees of freedom in T-Coupling group Water_and_ions is
79806.48
Reading Coordinates, Velocities and Box size from old trajectory
Will read till time 8
trr version: GMX_trn_file (single precision)
Reading frame 8 time 8.000 Using frame at t = 8 ps
Starting time for run is 0 ps
Opened nvt-normal2.edr as single precision energy file
Reading energy frame 8 time 8.000
Program: gmx grompp, version 2016.4
Source file: src/gromacs/fileio/enxio.cpp (line 1146)
Fatal error:
Could not find energy term named ‘Xi-0-Protein_LIG’
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
———————————————————————————-
P.S. nvt.mdp:
; Run parameters
integrator = md-vv
tinit = 0
nsteps = 5000 ; 10ps
dt = 0.002
; Output parameters
nstxout = 500
nstvout = 500
nstfout = 500
nstenergy = 500
nstlog = 500
nstxout-compressed = 500
energygrps = Protein LIG
; Neighbor searching
nstlist = 5
ns-type = grid
pbc = xyz
rlist = 1.1
cutoff-scheme = group
; Electrostatics and VdW
coulombtype = pme
rcoulomb = 1.1
vdwtype = cut-off
rvdw = 1.1
; Temperature coupling
Tcoupl = nose-hoover
tc-grps = Protein_LIG Water_and_ions
tau_t = 1.0 1.0
ref_t = 300 300
; Pressure coupling
Pcoupl = no
; Velocity generation
gen_vel = no
; Bond parameters
continuation = yes
constraints = h-bonds
constraint-algorithm = lincs
lincs-order = 6
lincs-iter = 2
(from redmine: issue id 2301, created on 2017-11-24 by gmxdefault, closed on 2017-12-11)
- Changesets:
- Revision a61e5a26 by Berk Hess on 2017-11-28T09:50:41Z:
Extend grompp missing energy term message
Fixes #2301
Change-Id: Ie28dcdb1d9f4100a9b4389f8d060b0f0749ec401- Revision f8c70b1d by Berk Hess on 2017-11-28T13:36:22Z:
Update documention of Nose-Hoover output
The documentation of Nose-Hoover chain variable printing was
(long) outdated.
Refs #2301
Change-Id: I2ef02e676141000937fedecf096b635ee2e69281