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 a61e5a26061880f26998f1ef1bcab5cf113c4d57 by Berk Hess on 2017-11-28T09:50:41Z: ``` Extend grompp missing energy term message Fixes #2301 Change-Id: Ie28dcdb1d9f4100a9b4389f8d060b0f0749ec401 ``` * Revision f8c70b1dfc93a264da00bcb19b827d5ac60dec06 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 ``` * Uploads: * [group_grompp_NH_energy_error.rar](/uploads/f7ecd201c238f67fe34d3b1c4c4fbd10/group_grompp_NH_energy_error.rar) * [group_nh_bug.rar](/uploads/234f792a679f263aeffce331862dfa1e/group_nh_bug.rar)