[gmx-users] MD simulation error : rRNA simulaion

[Hemant Arya]

Dear gromacs,
Greetings
I am trying to run a NVT with the following command.

My mdp file is below

title       = Protein-ligand complex NVT equilibration
define      = -DPOSRES  ; position restrain the protein and ligand
; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 50000     ; 2 * 50000 = 100 ps
dt          = 0.002     ; 2 fs
; Output control
nstxout     = 500       ; save coordinates every 0.2 ps
nstvout     = 500       ; save velocities every 0.2 ps
nstenergy   = 500       ; save energies every 0.2 ps
nstlog      = 500       ; update log file every 0.2 ps
energygrps  = Protein Non-protein
; Bond parameters
continuation    = no            ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type     = grid      ; search neighboring grid cells
nstlist     = 10         ; 10 fs
*rcoulomb    = 1.0       ; short-range electrostatic cutoff (in nm)*
*rvdw        = 1.4       ; short-range van der Waals cutoff (in nm)*
; Electrostatics
coulombtype     = PME       ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 4         ; cubic interpolation
fourierspacing  = 0.16      ; grid spacing for FFT
; Temperature coupling
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc_grps = Protein Non-Protein    ; two coupling groups - more accurate
tau_t       = 0.1   0.1                     ; time constant, in ps
ref_t       = 300   300                     ; reference temperature, one
for each group, in K
; Pressure coupling
pcoupl      = no        ; no pressure coupling in NVT
; Periodic boundary conditions
pbc         = xyz       ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = yes       ; assign velocities from Maxwell distribution
gen_temp    = 300       ; temperature for Maxwell distribution
gen_seed    = -1        ; generate a random seed



Error :

GROMACS:      gmx grompp, VERSION 5.1.4
Executable:   /home/amouda/Desktop/gromacs-5.1.4/build/bin/gmx
Data prefix:  /home/amouda/Desktop/gromacs-5.1.4 (source tree)
Command line:
  gmx grompp -f nvt.mdp -c em-steep.gro -p trp.top -o pr-nvt.tpr -n
index.ndx

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.17#

*ERROR 1 [file nvt.mdp]:*
*  With Verlet lists rcoulomb!=rvdw is not supported*

Setting the LD random seed to 2859163501
Generated 20503 of the 20503 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 17396 of the 20503 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'RNA_chain_1'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA'
turning all bonds into constraints...
Setting gen_seed to 1604041440
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet


When i gave equal parameter to coulomb (1.4) and rvdw (1.4) then it shows
different error
like
"Fatal error:
Group Protein referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp."


Please help me to solve the problem.
Thanks
-- 
*Hemant Arya*
Research Scholar
UGC-RGNF
Centre for Bioinformatics,
School of Life Sciences,
Pondicherry University
Kalapet
Puducherry- 605014
INDIA
Contact No. +91 9597221248
                   +91 2930-244141