[gmx-developers] Fw: [GROMACS - Bug #2301] (Rejected) Group cut-off scheme grompp error: Could not find energy term named 'Xi-0-Protein_LIG'

[Mark Abraham]

Hi,

Thanks for the message. Please do see the thread on Redmine - Berk has
already realized that he misunderstood an aspect, and is seeking more
information in order to see if we have something to fix.

Mark

On Sat, Nov 25, 2017 at 2:51 PM Du, Yu <duyu at sioc.ac.cn> wrote:

> Dear GMX Developers and Prof. Hess,
>
> I have said in the previous redmine post that I didn't change the
> temperature coupling. Both nvt and nvt2 use nose-hoover thermostat.
>
> I don't think this rejection is acceptable. If you need some additional
> information, please let me know.
>
> Thanks.
>
> Yu
>
> --
> Du, Yu
> PhD Student,
> Shanghai Institute of Organic Chemistry
> 345 Ling Ling Rd., Shanghai, China.
> Zip: 200032, Tel: (86) 021 5492 5275
>
> -----Original Messages-----
> *From:*admin at redmine.gromacs.org
> *Sent Time:*2017-11-25 04:30:22 (Saturday)
> *To:*
> *Cc:*
> *Subject:* [GROMACS - Bug #2301] (Rejected) Group cut-off scheme grompp
> error: Could not find energy term named 'Xi-0-Protein_LIG'
>
> Issue #2301 <http://redmine.gromacs.org/issues/2301#change-15383> has
> been updated by Berk Hess.
> ------------------------------
>
>    - *Status* changed from *New* to *Rejected*
>
> gmx grompp -h tells that -e is for read temperature (and pressure)
> coupling variables. Because you change the temperature coupling algorithm
> the variables changes (the types, not values), so you get an error.
> ------------------------------
> Bug #2301: Group cut-off scheme grompp error: Could not find energy term
> named 'Xi-0-Protein_LIG'
> <http://redmine.gromacs.org/issues/2301#change-15383>
>
>    - *Author: *Yu Du
>    - *Status: *Rejected
>    - *Priority: *Normal
>    - *Assignee: *Yu Du
>    - *Category: *preprocessing (pdb2gmx,grompp)
>    - *Target version: *
>    - *Affected version - extra info: *
>    - *Affected version: *2016.4
>    - *Difficulty: *uncategorized
>
> 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
> ------------------------------
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