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

Sun Nov 26 03:05:23 CET 2017

Hi, 

I have uploaded related files to the thread. Please check.

Yu

-----Original Messages-----
From:"Mark Abraham" <mark.j.abraham at gmail.com>
Sent Time:2017-11-25 23:50:46 (Saturday)
To: gmx-developers at gromacs.org
Cc: GMX-developer <gromacs.org_gmx-developers at maillist.sys.kth.se>
Subject: Re: [gmx-developers] Fw: [GROMACS - Bug #2301] (Rejected) Group cut-off scheme grompp error: Could not find energy term named 'Xi-0-Protein_LIG'

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 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'
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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